While most secularists take the establishment clause to mean that religion should not interfere with government, read in the context of the whole amendment it should be read to mean that government should not interfere in the affairs of religion (just as govt should not interfere in the affairs of free spech, the press, the right to assemble or petition).
Well, the buzz in Catholic circles is that the Obama administration is working behind the scenes to quiet Catholic bishops regarding the abortion issue. In particular, it concerns ArchBishop Burke and others who have commented on whether or not Kathleen Sebelius (Obama nominee for Health and Human Services) is fit to take the Eucharist. The rumor is that the Obama administration is pressuring the Holy See to silence these outspoken bishops, or at least pressuring the See to distance itself from their remarks.
Now, you might think it is silly for Catholics to argue that some Catholics ought not take the Eucharist because of their political views (support for abortion). But whether that is silly or not is not the issue. The Catholic Church is free to be silly if it wants. The issue is whether or not the federal govt should be meddling in the internal affairs of a religion for political ends (namely, to buttress support for Obama with Catholics by downplaying the pro-abortion stance of his nominees).
My view: The Church has every right to butt its head into government affairs – it is a free marketplace of ideas and any religious or non-religious point of view has an equal claim to participate in that marketplace. But the govt has absolutely no business (up front or behind the scenes) in trying to quiet certain voices within that public square. THAT is the real meaning of the First Amendment.