I'm well aware of that court decision. I'm an accountant, and until a few years ago I was closely involved with some of the business operations at a church we attended. The decision you referenced regarded tax treatment of for profit businesses by religious organizations. It boils down to the fact that you can't claim relief from taxes on normal business operations (such as selling books or magazines) under the guise of religious activity. This is why the WTBS went to the donation arrangement, they aren't selling anything, therefore it is a nontaxable event. In other words the decision dealt only with financial matters, not church policy, doctrine or administration. This is clearly within the authority of the government.
My comment about recent court decisions is based on the Citizen's United Case, which determined that corporations have the same First Amendment rights as people.
There is a logical fallacy at the heart of what this petition is attempting to do. In the name of religious freedom it would have the government determine what a church can or cannot teach. This is clearly prohibited by the First Amendment protection of the free exercise of religion. My point is not that the government can't remove tax free status from a church, it is that it can't do so based solely on doctrine or administration. It can remove tax exempt status based on economic activity (you can't pretend your business is a charity and the IRS has rules for making the determination). The government could, if it wanted to, remove tax relief from ALL churches, but I suspect it would have to just give up on the idea of tax relief for ANY charity in the process. What it can't do is remove tax relief from religions it doesn't like, or those that don't teach some acceptable set of beliefs.
And who gets to decide what is a cult?
I hate to break it to those looking for simple institutional solutions to groups like the Watchtower, but I don't think it can (or should) happen in this country. It will take a lot of heavy lifting, but the way to fight these groups is by shining the light of day into the dark corners. It takes time and hard work but we'll bring people out one at a time.