Back on topic, though:
I will agree that should it be shown (and probably will) that law enforcement did not act sooner against the FLDS because of fears of first amendment conflicts, then something needs to be done to better define the relationship between religion and secular authority which allows action to be taken when a religious sect starts doing things like sexual abuse of children.
But in doing so, we need to tread EXTREMELY carefully. In spite of the first amendment, our history is full of examples of religious sects being legally persecuted for daring to operate outside the accepted norms of the time. We cannot afford to repeat such instances. Allow even a scosh too much secualr authority over religion and somewhere someone will take the opportunity provided to abuse the authority and use it against whatever religion they find most objectionable.
As for the taxation issue, what would be accomplished by removing tax exempt status from churches? First it would increase the expenses of a church, by adding expenses like property taxes and revenue taxes. Second, withdrawing tax deductions for church offerings would reduce the amount of offerings. Something that "tax it!!" liberals seem to forget is much of the population do not have a significant amount of excess income - if any. If they pay taxes, it's that much less that can go elsewhere, including churches. So you have the dual penalty on churches of increased expenses and reduced revenues. The result of that would be devastating for small, poor churches who are barely able to meet expenses. Churches which are better off would have to cut back on their assistance programs.
And what GOOD would come from getting taxes from churches? Increased government revenues to spend on their own screwed up, wasteful programs, pay raises to congress critters, government sponsored research into the flow rates of ketchup? Sotty, but damned few people would argue the government would make better use of the money than the churches do.
Yes their are charismatic sects in which the leaders become rich by abusing the tax exemptions granted to religion. But the vast majority of churches do NOT abuse that relationship. Of all the religious leaders in this country, there are darned few that are above middle class economically. In fact I'd bet the majority would fit into the lower-middle or even low class sector of the economy. Do you really want to punish all for the transgressions of and extreme few?