I hope you don't mind me starting a discussion on your mod page, but I figured it might be a better place to talk about this. Also, it's actually easier to see for people stumbling upon your mod that there's a discussion taking place, since the thread should be visible below the mod's description.

So, scaling the rewards actually sounds pretty good to me. You could start very low, since even low percentages on science or a mere 50 society research points are a big deal at the very beginning of the game. Later on, I'd honestly not go out of my way to get the same reward.
This mod shouldn't really be about the rewards, though. It's about being able to keep tabs on the primitives. The asset tracker can also do that for you, but in a slightly less comfortable way. If you offer rewards, there's a high chance that people will want to finish the projects for the rewards and thus lose thee situation log entries reminding them of the primitives. That's a bit counter-intuitive, isn't it?

So, in my very own, very personal opinion the reward for researching the project should be a mere token. I'd be operfectly fine without any reward, but if we look at it from an immersion angle, it could be something like 10 society research points or so. Not percent on research, but actual research points. 10 to 15 is what you usually get from debris on engineering and physics, so it could kinda reflect that and be argued to be about what your scientists learn about biodiversity when studying several different species in comparison or something like that.
That way it would make it feasible to keep the projects until you're ready to start uplifting or have decided that you don't wanna with a particular primitive or have taken any other steps to deal with the planet in question - or the issue has been solved, because another empire has taken over the planet and done whatever with it.
To me this would actually be the preferable option. The projects itself are the reminder and I do them to check them off my list, the reward not being of any significance. Which is only possible if the rewards are pretty much worthless. Otherwise - risking getting repetitive here - people will do the projects for the rewards sake and get rid of the reminder for the primitives in question, which is the sole purpose of the mod.

You could of course offer a version for people who just want some more random rewards they have no influence over, becasue you never know how many primitives you encounter and when or where. I wouldn't call it a cheat, but it would make the game easier. With high rewards and luck in finding some primitives very early on even considerably so. I mean, imagine a 10% boost on the speed of the New Worlds research right away, like a scientist with the appropriate expertise gives. That's months saved. Who wouldn't make use of that?
It'd be a different mod, though. It wouldn't be about remembering the primitives anymore, but about encountering them quickly and reaping the rewards at the perfect moments.

As for the clutter in the sit log, I wouldn't worry about that too much. Yeah, you have a lot of debris in there after a war, but that times out while primitive don't. So it's gonna be up top, right below the story quests after a while. You also can get rid of each and every one by finishing the project, essentially sorting out all primitives you don't need any reminders of. Looks like that's the best modding can currently do about the issue.
Just make sure you have the 'track on map' and 'go to' button included, the latter of which being the one making this more comfortable than the Asset Tracker. That#s actually what I want out of a mod like this. ;-)