Everything you wrote is absolutely true. However, it doesn't address the problem of a church, not a person expressly endorsing a particular candidate. The difference is that a citizen isn't a tax-exempt institution, and a church is not a citizen.
The constitution does, absolutely protect the free speech rights of citizens. But there is no constitutional guarantee that a politically active church can remain a tax-exempt institution, while the members of that church can say whatever they like, that's guaranteed.
"Everything you wrote is absolutely true. However, it doesn't address the problem of a church, not a person expressly endorsing a particular candidate."
A church is a voluntary association of people, most of whom are usually citizens. By what argument do those people lose their right to political speech through organizations to which they belong? By what authority do they lose their right to say, "We of the Lutheran (or Baptist, or whatever) Church endorse Alan Keyes"?
"a citizen isn't a tax-exempt institution"
And since when does the tax-exempt status of churches have conditions other than that they are legitimate churches? Their tax-exempt status is not some socialist attempt to encourage them, as it is with non-religious tax-exempt groups. It flows from the First Amendment...a tax is a restriction on freedom of worship. Their tax-exempt status is constitutional, not granted at the whim of IRS reprobates.
"But there is no constitutional guarantee that a politically active church can remain a tax-exempt institution, while the members of that church can say whatever they like, that's guaranteed."
I think my last paragraph dealt adequately with that argument.