Make ways to cap the income then. For example, temple estate efficiency = % of followers. If a lord is willing to give s significant portion and income to a religion to build a temple, what makes you think he wouldn't have donated under the current system anyways? Plus, the temple could be taxed just like any other estate, could fall prey to looting, and even maintenance fees could be there.
Any large cash flow IS a donation from a lord anyways. Plus, with this setup you wouldn't likely see many temples generating high income either- it's too much commitment and risk for any but devout lords. The only placed you'd see it more prevalent would be where religions are already the dominant force, politically, such as theocracies.
