The FACE Act is what they use to protest people praying outside of abortion clinics (and is an abomination), and the KKK Act was created to go after the sort of people who blew up churches and hanged ...
Stampeding a church and harassing parishioners is a severely greater offense than protesting outside of an abortion clinic or even rioting at a government building, in my opinion. It is in the spirit of the first amendment to protect the sanctity of worship by prosecuting those who would violate it.