Prayer in the legislature is a silly tradition that should be abandoned, but until that happens, the government should at least treat all religions equally. Yesterday we saw a step in that direction: for the first time, a Hindu led the opening prayer in the U.S. Senate. And a Christian right group disrupted it.
It seems that the visitors who disrupted the prayer came to the session for that very purpose, which makes their case far weaker than if they had to be there and were exposed to religion they disagree with against their will. And they are self-centered hypocrits, because they are eager to foist their religion on others, just not willing to hear a word of somebody else's faith. Yet, I don't think they should be punished; I think they were legitimately exercising their First Amendment rights.
One of the reasons government should not endorse religion is based on the following problem: a lot of people have very deep feelings about religion, any given religion is false to many (actually most) people, and no objective standard of truth applies to religion; therefore, whenever government endorses any religion, it just pisses off a lot of people without any good reason. People don't like it when the government - which has power over them - endorses what they see as a false god. And they have a right to not have the government do it.
That applies to everybody. Those fanatics may be idiots, but they have the same rights as everyone else. For one day, the government has implied, through a meaningless and unnecessary ritual, an endorsement of a religion that those people deeply feel is false. Why shouldn't they protest against it?
Of course, every day except yesterday, the government endorses, in the same way, another religion. The only difference is that those people like that other religion. But there are others who don't, and they should have the same right to protest. Those Christian activists gave us some good evidence that prayer in the legislature is harmful. They probably didn't think about the ramifications of their heckling, but it may have been a step toward the end of Congressional prayer (which would mean we saw two steps in the right direction).
And they don't have a right to deny others the same rights they have. So next time somebody interrupts a Christian prayer shouting that it's about a false god, the Christian right should shut up and put up with it.
UPDATE: Hindu prayer was offered in Congress once before, in the House of Representatives. Family Research Council made a stink then. There is a good blog post about yesterday's incident on Pharyngula; comments #6 and #50 there are also noteworthy.