There was an attempt, way back when, to revoke the tax exempt status of All Saints Episcopal Church in Pasadena, CA because the priest there was openly critical of the Bush administration. The argument was that, by criticizing Bush he was endorsing a Democratic candidate and churches at the time were not allowed to endorse political candidates. Of course, Trump changed that (and, possibly, his only legal leg to stand on in regards to this threat). Unless there’s an amendment that makes space for “not hurting Twumpy’s widdle feewings” then, yeah, I don’t think there’s much he can do to pick on particular denominations, etc. But with Trump, nothing is assured.

EDIT: I see on the original post that Trump’s statement that he removed the clause forbidding churches from endorsing candidates is actually false. Welp.