A couple of my friends complained that you cant play this game in a clean style, which is true for a very black and white approach in that being a white knight is going to get you killed.
However a somewhat 'mature' approach to the idea of doing good can get you through the game without you feeling like the worst cop ever.

This is firstly a general guide on how to survive the demands of groups on you with as little corruption as possible. I also included a few specific hints on major storyline events in the spoilered bits, they are tricky to navigate without going off the rails as it were and becoming a 'bad guy'

This is not a happy city, an angelic cop in this position is probably screwed, remember the real history of the mob in it's various incarnations through our history. So we are going to have to bend a little, some slightly-foxed washed-last-year heavenly vestments, a grey stetson, take your pick.

It is possible to survive the attentions of the mob without resorting to killing innocents yourself and to appease city hall without trampling human rights.
Greater Good, remember?

There are three main parties you have to keep happy in order to get your job done, by which I mean; protecting the citizens, your officers (and their jobs) and yourself (and your job/bank account/life). Those are the city bureaucrats, organised crime and your officers.

'But I don't work for the mob! I'm super-clean'
Tough, they think you do, which ultimately is all that matters, gotta stay alive, greater good.

Let's start with the 'good' guys. You will get requests both from city hall and from the mayor. Now while it is city hall that you apply to for expansions to your force the mayor has major weight on their decisions, so you have to keep both pretty sweet. Unfortunately just because they are politicians doesnt mean everything they do is legal (d'uh) so you want to think about how to handle what they ask for.

We need to keep them happy both because they approve requests, but also because they can cut funding (job slots) if your performance is low (fail/ignore too many assignments and/or lose officers/civilians on the job). Manpower is the keystone here, the job assignments from the city/mayor can pop with no warning and some require immediate commitment, so keep men on hand. In order to keep our noses clean we can ignore outrageous demands that may lead us into legal issues and instead turn up to all the PR style nonsense they inevitably ask for.

But manpower is a vicious circle, if you get it wrong and people die and/or you disappoint the bureaucrats then your workforce will be slashed and all of the above becomes even harder. Do not fall off the wave, keep your staff counts up.

Example City Hall Requests that will get you into trouble (not-necessarily exhaustive):

Fire Black Employees: Theres no reliable way to do this clean, you cant fabricate a legal reason for the two detectives and may face prosecution.
Supress Peaceful Demonstrations: Theres a few of these, but you just cant use force on peaceful citizens no matter what the parties are telling you, you would have to frame someone.
There are ways to redirect legal issues, but thats not very clean so just go ahead and stick to your guns, you don't have to do everything they ask make up for it opening a mall or whatever. Since both the mayor and city hall tend to unite on the most troublesome issues its a big standing hit though, to keep your job slots safe keep them as happy as you morally can.

Now the 'bad' guys. Ok, probably didn't need the quotes there these dudes are pretty bad.
Simply in order to stay alive, at some point you are going to have to somewhat acknowledge and pacify these gun-happy lunatics. It's unfortunate, but otherwise they are just going to have you killed and nobody benefits, so here comes some real stretching of morals.

They will offer you a variety of jobs directly, and may occasionally notify you that a crime is going down at a particular time along with a bribe to keep out. Firstly we want to pick carefully through the jobs they offer, not all of them involve your officers committing crimes, mostly we are talking about misuse of resources, some abuse of position and so on. We can handle that. Some of their requests quite honestly warrant police response which makes life easier.

Much like city hall, it's a light-touch. Do as much as you can while politely declining the invitation to bash some skulls, thankfully there are a range of less aggressive compromises available.
You may also get the opportunity to 'lose' evidence in certain cases and send it their way. This makes you some money, but it also makes them a cut, and this seems to please them a bit, which longterm feels morally a step above cops doing goonwork. You might want to be picky about what they get but sometimes the story behind a case helps you justify a little boost. Unfortunately the best earners are the hard drugs. Guns you shouldn't bother with anyway, they dont earn much. Jewellery is good now and then.

When it comes to ignoring the jobs they want ignored, well, you don't have to if you have been managing to do a few odd things for them. You might ignore a couple of thefts or similar but bust them everytime a civilian is at risk, and with enough background work as above, keep your life.

And finally the thin blue line, your men.
You really really want to keep your men happy. Firstly it makes them more likely to show up for work at all. Secondly they are less likely to plot against you and report you for the various small crimes you are committing along the way.
There are a variety of methods in the game for this. Barbecues and so on, but the clean player doesn't actually need to worry as much (besides, they cost). If you are not constantly in the mobs pocket, or illegally firing staff left and right then they shouldn't mind the odd thing or two being a bit...well, iffy.

It's possible to hire a snitch in the ranks to keep you informed, but they mainly point out who is filing a complaint, which isn't an issue if you don't provoke any. Ever seen a snitch in a movie? Don't use your best/favorite cop, just incase like.

Keep them alive, keep their numbers up. That way you can respond to more incidents with better numbers for increased survival and even grant the odd day-off sob story. Finally pay attention when decision windows pop-up for jobs. You can easily get your officers or civilians killed with the funny options (and yes, some are pretty good), think like a cop, be cautious but not unjustly aggressive. Overuse of force can get you into trouble. (Basically fairly standard attitude. You can usually justify shooting anyone aiming a gun who isn't holding a hostage, knives are fifty-fifty, you can often taze but shoot if you think an officer might die.)


Ultimately it's important for the clean cop to be able to balance these three parties. If you let the mob run wild then people die and keeping city hall happy is harder without getting a bit dirty. If you slave to the politicians you end up in court and survival is hard without getting dirtier. Upsetting your officers winds you up in-front of the prosecutor or spending your own cash to keep them happy and quiet. Walk the line.
Specifically, you can do enough to stay in city hall's good books, off the mafia hit-list, make bank, never need a BBQ or snitch, yet never be investigated if you can find that thin grey path through the story. Just corrupt enough. If you do too much, your men will start to get agitated and a spiral of spending money and taking dubious actions to stay afloat begins. Remember they are cops!

As you will swiftly find anyway in the story, Jack is saving for retirement. So your personal wealth is an issue. One of the problems with clean play of course is that theres less money to be made.
It is slower in the beginning, yes. There is plenty of time to make your cash in an honest way through the story so don't worry about it, it's possible thanks to rewards for high-profile arrests.
This turns out infact, to be the least of your worries.

Pay Raises: This is a tricky one. Your weekly pay is pretty poor in the scheme of what you want to make, and asking for a raise gives 10%. So logically you would want to grab it early and stack it up, but there are no doubt other things you want too and you dont want to push it or risk them denying the lot and you losing a week of expansion. The way the story escalates means you are going to be leaning heavily on swat by about day 30. You want at least 1 rank of endurance fairly early and increasing their effectiveness lets you send fewer general men on heavy calls which is win all over. Powerful upgrade.
Light Corruption: You actually make a reasonable amount doing stuff for various companies in the city, pick the legal stuff (yes its all misuse of time, but not all have you intimidating or worse). Your cut from stuff to the mob wont amount to much, since stealing too heavily will probably stir up your officers.
Rewards: This is actually where Jack has the opportunity to make some big sums of money. It will be a little while before the big ducks fly into range, be patient. Let's just say theres lots of white money eventually if you are good and quick enough to catch it all.

Mob War -Theres an inevitable mob war starts that you get pretty much dragged into. Like I said above, not up to you whether you play their games. You end up with the option to pick sides, between the first gangsters you met and the upstart.
It's nigh-on impossible to back the new guy and maintain any kind of clean conscience, it works as a kind of double-agent mechanic that results in you juggling both, and sooner or later you will run out of legit ways to please one of these psychos. Devil you know makes an easier ride for the hard-pressed good guy.

Serial Killer - A serial killer pops up fairly early and you have the option of keeping the case from the Feds, this has the potential to make Jack some serious money. It's not possible however to keep the case to yourself without having 2 officers killed by the mob (one who threatens to snitch and 1 innocent who unfortunately you must also trap since officers wont patrol alone at that point). This is a bit black for the ethics I'm describing here and while it's a lot of money, you can make that elsewhere sooner or later.

Take down the Mob - You get the chance to take down the mob in the city, which you should totally do to justify all the grubby stuff and since it gets you a serious reward. Don't forget to keep them happy throughout the investigation though, they are dangerous cats.

It's not easy. To be honest it's probably harder than crooked since there are plenty of mechanisms to help you play dirty and get away with it, though they do involve throwing money around. Playing clean is all about finding the balance. Tread just right and you dont have to spend money everywhere. Your cops never complain, city hall never denies your requests or cuts your staff and the mob just dont kill you. The money trickles in and you keep your soul.

Theres far more down the road, actors beyond those I mentioned who come into play and it gets harder and harder to stay in the right, but there is a knife-edge you can walk, be a realist, make comprimises and remember the greater good..