Hi, Logic.
I think you've got an interesting idea going here. If creationists use the "balance" argument to get creationism into schools, their unwillingness to teach science (not to mention other religious and philosophical ideas) in church kind of constitutes a double standard.
Problems come in when you consider that the ID movement is working hard to make people believe that they are a legitimate science that is not strictly tied to Christian theology.
Also, like Moose said earlier, you have to consider that schools are public institutions, whereas churches are in the private sector. Each system has its way of allowing the individual members to decide what goes on. If you want something different taught in schools, you have to petition and/or vote accordingly, etc. Religion has a way of letting you choose what you are taught, too: you go to a different church somewhere.
Religion has always enjoyed all sorts of immunities, at least in the USA. They are in the unique position of being shielded from attacks from anywhere while also being allowed to meddle in anybody else's affairs by simply claiming that it's part of their belief system. They are permitted, by law, to attack science, but science is not given entirely the same privilege to fight back, except in blogs and seminars. For instance, if a scientist wished to protest the activity of a certain religion in his hometown, he would not even be allowed a hearing in the local court. But, religion protesting the presence of science in its hometown can make it all the way to the Supreme Court of the United States.
It's unfair. But, really, if you think about it, that's the way science is: the scientific method allows anybody to challenge anything at anytime, and that's why science is so strong. Ironically, the protection that religion has gotten under the US Constitution is the reason why it will never have the strength of science, because it will never have to overcome the challenges to its central axioms that science experiences every year.
-Bluejay
Darwin loves you.