The simplest solution would seem to be to end tax exemption for any group that exists to propagate *any* particular religious or political ideology. It would keep the government out of the church and effect everyone equally - every religion, every political organization.
As far as "freedom of religion" goes - there are limits to what kinds of activity are protected as "religious expression." Some groups have claimed that using drugs is part of their religion; others have claimed that animal sacrifice is part of their religion. The First Amendment does not mean that you can do anything you want and claim that it is okay because it's part of your religion.