Church vs. State?

It was revealed Sunday that the IRS is currently targeting the church that I attend, All Saints Episcopal in Pasadena, for removal of tax-exempt status. (read about it here) About a year ago, the former rector gave a sermon that used a hypothetical debate between Kerry, Bush, and Jesus. Basically, the sermon gave the opinion that the war in Iraq is wrong and had Jesus questioning Bush's foreign policy. At no point, however, did Rev. George Regas actually give an endorsement of either candidate, he only urged the congregation to consider the teachings of Jesus and to vote with their conscience.

The issue at hand is that non-profit groups are not allowed to "intervene in political campaigns and elections." So the letter warned that the IRS would be investigating.

Question: What church does not speak up about political issues? I know that the Pope has come out against the war on many occasions, but is the IRS going after the Catholic Church. Consider this: All Saints is nationally known for being a very liberal church as well as being active in pursuing human rights. Although the church's tax lawyer seems to feel that the IRS's actions are not politically motivated, I don't see how they are not. At what point does speaking out against war not fall into the realm of any church? How is it "intervening" in an election if there is no actual endorsement? How can Bush openly proclaim his strong religious beliefs and at the same time see the IRS do this?

I realize that I sound a little to much like a conspiracy nut, but what do you expect? I am going to try and do a little research into other church's that have tax-exempt status and make strong political statements. I'm looking at you Pat Robertson! (Seriously, I am. His TV channel got into trouble back in the 90s).