The sentence is logical, you’re just incorrectly assuming it’s a simple syllogism. The OP isn’t saying that churches need to be treated substitutably with members of the church. But it’s apparent that churches as entities need to be protected in order to protect individual religious freedom. If the government banned mosques (as legal entities) from constructing buildings and holding gatherings, that wouldn’t ban Islam, but it would obviously be an impingement on the religious freedom of Muslims.