Religious Freedom

The event that prompts this post is, I'll admit, a bit outdated. Remember that raid on the Fundamentalist Mormon sect (known as FLDS)? Let me recap for a second in case you forgot. A teenage girl called an anonymous tipline to say that she had been abused on the ranch (Yearning for Zion, I believe it is called, if you'd like to wikipedia it). Alright, so that was good, right? She worked up the courage to call out whomever this asshole who abused her was, and hopefully he will be thrown in jail.
But no. Instead, the next day, the powers that be invade the ranch, and take over 400 children away from their families! Because of a phone call?
Think about a regular community, like Traer, or in Ohio like Berea. A girl is abused and calls the proper authorities. Would the police raid every home in the town and take away all legal minors? Hell no!

What I am saying is that I am with the FLDS on that case--apparently the Supreme Court of the state of Texas was, too. One phone call does not warrant taking hundreds of children away from their home. It was, clearly, an issue of religious discrimination. People think the FLDS is bizarre (which it is), and maybe even barbaric, because they allow polygamy, and they pretty openly think men are better than women. Not to mention, they tried to go off and live on their own! How dare they!
Well listen, the fact is, just like freedom of speech, when you have a country with freedom of religion, you have to let the weirdos in.
The state claimed their right to take away the children, because they feared them being 'socialized' to become abusive. The courts rejected this as too broad.

Ok, so thats my opinion on that case. But it brings up some interesting questions about freedom of religion that I just don't know the answer to.
Freedom of speech laws have had many famous court cases to sort how far it goes. Basically anything that isn't obscene (as defined by the Law) is free. But what about freedom of religion? It seems intuitive that we would want a vast range of freedom of religion--but then cases like the FLDS weaken those intuitions. Religious pacifists don't have to fight in wars; this seems fair. Can a religion be openly racist? I would say that should probably be allowed, for similar reasons as freedom of speech. Where do we set the limits? Any suggestions? We can play it safe up in abstract theory land to simplify things.

The second question I have is about organized religions vs. non-organized religions. If the law is willing to grant religious people exceptions from obligations, which they ought to, why can't irreligious people have the same perks? Ok yes, you shouldn't get to avoid draft because its inconvenient, but that isn't exactly what I'm saying.
What I am saying is that, I don't belong to any religious group. But I have ethical standards I take just as seriously as devoutly religious people. Why should I be legally obliged to do something I consider unethical, if religious people don't? And how many members does a church need to have before their beliefs are accepted?
Certainly we can imagine strange religions which would bring serious problems--like a religion which had a compulsory communion of LSD or another illegal substance. The government has let this type of thing go with certain Native American religions; why couldn't a new start-up religion be just as valid?
I'm not asking these questions in order to cheat the system--I'm just trying to consider a principled way to give equal rights to all religious and non-religious people, regardless of their particular faith's popularity, normality, or age. And this question is proving more difficult than I thought it would be. Any takers?