I would re-up the funding on faith-based programs; but I would also put secular programs on the same level playing field. Additionally, I would also pass legislation requiring that all faith-based organizations - think tanks, PACs, anything with any part of their mission or origin being non-secular - must put the name of their faith into their name. So the "Thomas More Law Center" would have to call itself the "Christian Thomas More Law Center" in any material publication and any kind of faith-based abstinence program would have to be labeled as such as well. "Christian Pregnancy Counseling". "Islamic Lending Group". "Scientology Publishing Ltd." "Unification Church Hammerstein Ballroom" and "Unification Church University of Bridgeport" and "Unification Church Washington Times." And so on. Full and utter transparency in all things, so you know of any potential biases that could come from any organization.
Any organization that operates under false pretenses - masquerading as a secular one but promoting their religion - would instantly have all funding removed. Why wouldn't they want to boost their religion's brand with a big, bold label? Why would a faith-based group even want to pretend to be secular, if not to be intentionally deceitful about evangelizing or converting worshippers through "good works"? Good works are supposed to be their own reward, no?