That does sound silly and contrived. Modern Christians don't take the second Commandment as far as Jews and Muslims, so there's really no basis, except for fear of conversion, to forbid entering another denomination's church.
But with the Jews and Muslims, it's about idolatry.
My religion is against homosexuality, but I don't notice the court allowing me to be offended by that and outlawing the behavior.
Some day soon in San Francisco a public school will have its graduation in a gay bath house, and then you'll have a good case. I have no problem in general with a graduation being in a church. But in this case a public institution's choice of venue basically told a student he couldn't go to his own graduation. I do see a problem with that, but they should have been able to settle this reasonably.
But that is there problem, not mine. Why must I be punished because of their belief system, when I cannot make them be punished because they don't agree with me? That is the crucial question. Why is it one sided? In case you don't know (and apparently you don't) Idolatry is also forbidden to Christians, so what in the heck would be in a Baptist church that would bother anyone?