Unless the country's primary religion is on the line, you are not going against all religion - you are going against the specific religion in question (or religions). Systems resit change, so if you advocate for "let's not give this minority's religion equal rights, and instead take away the rights of the primary religion" only the first part will get implemented.

Analogy: Whenever there is a talk about legalizing same sex marriage, someone will always argue that the state should not get involved in any kind of marriage. Does this position have merit on on its own? Yes. But when presented in the contest of same sex marriage legalization, is it anything but pure support of continuing the oppression of same sex couples?