Regarding Metaphysical Resources
Aside from the obvious need for a facelift of some sort, I think a more reliable method of generating these resources would prove more beneficial than switching solely to belief in this area. Belief, as far as I'm concerned, should be for the active expression of divine power, whereas the accrual of metaphysical resources should pertain primarily to your empowerment and more substantial civilization improvements.

I think if you play well enough, the use of these resources could allow you to greatly accelerate the advance of your civilization over others, instead of acting as a design leash to mete out the pace of our progress.

These could be produced in a variety of ways, intermixed with belief generation (representing say, follower prayers/ideas, or what have you) and abode locations, through physical resource sacrifice/tribute, and so on. In general though, these would be passively accrued instead of actively gathered, and supposing they were generated in part by structure location, the construction itself could provide you with a fair amount of the relevant resource(s) with a small trickle of it thereafter.

Excess amounts of these resources could be used, as noted, to jump your civilization ahead or do whatever else you might like, customize the look of your land, the strength of your abilities, etc.

Regarding Physical Resources
In this area, I've made my ideas known, but I'll reemphasize them here, I think that much like the number of followers not the number nor size of abodes unlocks stuff in the timeline, so too should the amount of physical resources gathered unlock stuff. In much the same way that followers are automatically accounted for, I think resources should be automatically gathered. Similar to Black & White, however, if you want you can intervene to boost yield occasionally, but it would not be necessary.

In a similar vein, all incremental timeline upgrades (e.g. crop rotation/advanced farming, bigger abodes, voyage ship capacity, etc.) would be fueled by these resources not metaphysical resources. Metaphysical resources would concern say, the leap from mud to wood, but not what comes after nor in-between the two, this would be more follower-driven and would, in my opinion, make more sense and give followers more life.

By putting demands on the resources in this way, it would resolve the skyrocketing inflation problem produced by limiting them to the production and repair of abodes among other things, but wait, we've not addressed one other part that also inflates in the same manner. Followers.

Now we can be evil and say sacrifice them, but that creates another issue, a great drain on belief for minimal reduction in inflation. We need to consume followers in some way. There are a few ways to address this.

First, combat. They get into conflict, they die. Great.
Second, disease. They pollute the land, they makes themselves sick, they die. Great.
Third, sacrifice. We're tired of them, let's off them either for gain or to be rid of them. Okay...
Fourth, mortality. They last awhile, then they die. Great.

Personally, all of these sound appealing to me in some way, and could be given depth in various ways. Combat could be through conquest or insurrection, disease could be from your own pollution or others' sabotage, sacrifice could be overriding their will or self-sacrifice to transcend into metaphysical resources, mortality could lead to follower progression via experience or a greedy god that prefers high numbers with short lives to advance faster, and so on.

TL;DR: Divide the timeline into a cultural double helix of follower-driven civilization progression (physical resources) that you can loosely aid and guide, alongside a mutually complementary ideological progression (metaphysical resources) that shapes your powers without being over-burdened by more earthly demands. In this manner, you might be able to satisfy the interests of those more captivated by focusing on their followers while simultaneously satisfying the interests of those captivated by the idea of playing their own unique deity.