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.
These are both good ideas. A "tax free" amount would be nice. But 10-50 is nothing for even a moderately sized guildhouse or temple. It should be based on the size of the temple. For a level 5, I would say 100-200 is a reasonable sum to have tax-free.
The change to tax on income is also a very good idea. It preserves the ability of religions to stockpile cash, while limits the banking. I believe it should still be at a tax-preferred rate (maybe half or a quarter of the local rate), but it should happen. You could process it either during the transaction or weekly, I don't know which would be easier. But this is an excellent idea.