The church charities are the main refugee resettlement organizations, so I doubt they will be shut down. We’ve already seen the order on the totum pole after Orlando.
I hope Trump is able to cut off all government money to the churches. The Catholic Church was deliberately made dependent on government money by the homosexual Satanist Cardinal Bernardin. Starting in the sixties, as General Secretary and the President of the bishops’ conference, he got the Church involved in supporting Alinsky, contraception, pro-abortion politicians, No Borders—every evil you can think of with the POSSIBLE exception of actually paying for abortions DIRECTLY. At least, they haven’t been caught actually writing checks to abortionists.