You may never be able to regulate the content of religion but you should be able to regulate the context of it. The issue of taxation is very valid and I am all for the removal of such allowance. However, it is only a means of diminishing their power, not eliminating their ability to inflict influence that harms people.
The constitution broadly states that no law should be made against a particular religious belief or that limits religious freedom but it defines religious freedom to include a lack of belief. If no law should be made against religion, what can be said about laws that limit your lack of belief?
For example, when we make laws against abortion, we are favoring a particular belief. If someone was to establish a religion that granted the individual's choice to terminate a pregnancy under religious belief, would this be in conflict? Would the law be favoring one belief over another? Lets take this in theory, because we all know that preservation of life, is at the center of this particular example.
With that in mind, I see that we can not create law that regulates religious beliefs but we can create laws that create a context where the individual's right to choose is limited to certain principle. Just like we understand that abortion is/could be considered a crime and in the process favor a particular belief (the favoritism towards that beliefs is taking a secondary role in my analogy), then therefore we can allow, for example, JWs to exercise their freedom of religion but such should not extend to the point where exercising such freedom entails terminating someone's life, including your own. (like in the case of blood)