By granting churches a tax expenditure (which what an exemption is), would that not be a case of the government getting involved in religion?
No one is saying that the government should have oversight over what churches do. That would be a violation of the first amendment.
But making the tax expenditures the same as for other non-religious entities (corporations for example), would be more in line with first amendment position that the government should stay out of religious issues.
I don't see how making things the same (people being treated equally) could be considered infringement.
A most interesting issue.