Let the reader please understand that I believe that 1) you can be a Christian and be either a Democrat or a Republican; 2) both are guilty of selective readings of Scripture; 3) Jesus would find both political parties unacceptable; and 4) while we are a nation with a lot of Christians, we are not - and never have been - a Christian nation. In fact, I don't think it is possible to be a Christian nation anymore than it is possible to be a Christian rock or a Christian dog.
I see three issues at stake here.
First, while, under the Free Exercise clause (the second half of "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof."), it seems to me, churches ought to be able to preach as they please. However, one of the advantages churches hold is that they receive tax-exempt status. It is widely accepted that churches can lose their tax exempt status for political advocacy for candidates, and some now want that to extend to issue advocacy. I believe that at least the latter, and possibly the former, potentially run afoul of the Free Exercise and the Establishment clauses IMNTBH opinion. How? Well, as Chief Justice Marshall once famously opined (McCulloch v. Md., 4 Wheat. 431), “the power to tax is the power to destroy.” So if we destroy all the religions we don’t like, those who are left constitute a defacto establishment.
Certainly we want to prevent a political party from organizing itself around a pseudo-religious doctrine simply to enjoy tax benefits, but as the political debate in this country develops and changes, and that which was once taboo becomes the accepted norm at the behest of the Permissive ... oops ... I mean Progressive elements of society, the line here is not really between advocacy for candidates versus advocacy for issues. Rather the line becomes one between traditional expressions of morality (which civilizations have crossed at their peril) and permissive ... darn it ... I did it again ... I mean, progressive stances which set aside traditional morality. Since most traditional religions contain a moral behavior element to their teaching, those teachings are likely to run afoul of the political left. Yet these teachings are still a proper realm for religion.
***Second, if this is a matter of constitutional principle, then it does not matter what the presenting issue is, or who the parties are. If the use of churches to advance a conservative agenda in 2006 is of concern to Barry Lynn, then he needs to repudiate the use of churches to rally support for the 1960's civil rights movement, and he ought to file a complaint every time a Democratic candidate is shown on the nightly news speaking from a church pulpit during election season.
But he won't because the Rev Lynn (does he still claim that title?) is about as honest a broker in the church/state debate as Pat Robertson.
Further, we have a little history in the Valerie Plame Kerfuffle of the Left pushing so hard that they end up cutting off their own noses to spite the Right. If any right-wing activists start playing Mr Lynn’s game, you may see the rights of both parties curtailed, just as the press’s claims of privilege were when the New Orc Times decided to push for a full investigation of the Plame leak; they not only got their own reporter jailed, they got their wrists slapped by the courts and the notion of a reporter's rights defined and restricted.
Third, I have noticed a tendency, reported largely on conservative blogs, of the bureaucracy to try and sabotage the Bush Administration. It has been noted in the State Dept, the CIA and elsewhere. Could it be that some mid-level Clinton appointees / hirelings at the IRS are now trying to use the tax code to change the course of the country, much as Ms Plame recommended her husband to travel to Niger to do just the same thing?