They are limited to stating their position on issues only.
If the rules are limited to stating their position on issues only, why would stating you are against the war get a church in trouble?
It wouldn't. That's not what the IRS was investigating.
"In the sermon, Regas did not instruct parishioners whom to support in the presidential election but said that Jesus would have told the president that his Iraq policies had failed."
If the statement he had made was simply that "Jesus would have believed that war is wrong" the IRS wouldn't have any interest. Once the speaker invokes a name (or position that refers to a political persona) then they are outside the bounds of tax exempt organizations. That is what the IRS is looking into.