a) change the tax amounts - half taxes for guilds, and quarter taxes for temples. I could also add a "tax free" minimum amount, maybe 10-50 gold per size. That would give the temple some amount to cover regular expenses with that is not taxed.
b) change the tax type - I could store the amount of gold put into the treasury between tax days, and tax only that, i.e. turn it into an income tax. This would also reduce the lord = massive balance problem a little, but it would reduce income through guildhouses dramatically.
Either one of these would solve most if not all of the problems I see with taxing religions. My personal preference would be option a), but I think either would work just fine.
