When Gods are weak and forgotten...

Since we are just spit balling ideas I will toss out a few that came to mind. Granted they would certainly need refinement, but could helped spur you on! Playing off of your "preach" idea you could have it be a give to take kind of scenario where they are awarded spell points for each thing they do that they can then use, but they would still have the limit of the spells per day they can cast. ex: cleric goes to town and tells ten people about the diety, they now have 10 points, but at level one can spend all of those, so they might be good to go for a couple days. The other thing they could do is set up that altar, and you decide that 2 people per day see it, and now the cleric regens two spell points a day. You could also have that altar torn down, and add in the twist of "you don't feel the increase of power after resting" plot hook to go see why.

The other idea would be a spell failure percentage, and you could tone down the loss of the spell by instead making it minimum rolls with any dice involved in the spell. I love any chance to roll on the wild magic chart, but thematically that makes magic seem messed up rather than running low.

Those were the two quick ideas that popped into my head. Hope they help! Also, what kind of interactions are the gods having in this new realm, and what precautions are they taking to not be snuffed out by the evil guy?

I think there's a lot of stuff you can do narratively to emphasize the weakness of the gods without ever dipping into mechanical representation of the fact. I'd exercise caution in changing mechanics. Yeah, a fighter losing his favorite magic weapon and armor is hamstringed, but he regains most of his effectiveness once he acquires even mundane weapons armor. Acquiring a god (or rather, restoring one) isn't such a simple matter. I don't think your PCs are being equally inconvenienced with the systems proposed so far.

The way I would probably run this scenario is for the god to announce to the PC cleric (probably via dream or communion in prayer) that he must promote the faith. As long as the cleric is putting at least some effort into it, his magic operates normally... that is, the god is making sure his representative has the resources to perform his ordained quest.

Neglecting his duty would have consequences. I think I would begin by barring access to the highest level spells (while retaining spell slots to fuel lower level spells) unless they are used to directly promote the faith. I would generally make an exception for spells used in combat, as the god should be smart enough to realize a dead cleric can't promote the faith at all.

Briefly, it seems like you're approaching this as a matter of regaining spell utility, whereas I would approach it as a matter of retaining spell utility. Weakened or no, we're still talking about a god here. He can have enough juice to power a single representative if you feel that's fitting for your setting, and your player might like the "chosen one" schtick.