Oh please, if you're going to ascribe partisan blame for the politicization of the Supreme Court, at least go back to the very beginning. The Warren Court (1953-69) was easily the most activist in American history, and it usurped the legislative process to establish new, sweeping affirmative rights and severely limit State control of local political matters. It was the Warren Court that ruled prayer and the teaching of creationism unconstitutional in public schools, gave blanket protections to obscene speech, prohibited states from regulating access to contraception and of course, fortified civil rights and rights for the criminally-accused. Say whatever you want to about these cases on their merits, but these issues remain controversial political questions today (much less 50 years ago!) Liberals began politicizing the Court when they started using judicial review as a blunt instrument to cut citizens and legislatures out of the political process.
Of course, as William F. Buckley, Jr. said best, the job of the conservative is "to stand athwart history and yell stop!" There was new, conservative (neoconservative?) reaction to the Warren Court. In1968, Richard Nixon explicitly campaigned and was elected on a promise to appoint strict constructionists. After having two of his nominees rejected in 1969-70 by a liberal majority in the Senate (first time that had happened since 1894!), conservative William Rehnquist was confirmed by one of the narrowest margins in American history to date. The Federalist Society was founded as an "alternative legal elite" in 1982. It's no surprise that liberals sank the nomination of Robert Bork in 1987 - the same year the U.S. Senate allowed television cameras into its proceedings and Ted Kennedy delivered a fiery speech impugning Bork's character by calling him a segregationist and misogynist. Clarence Thomas' 1991 confirmation is the most recent time a Senate controlled by an opposition party has approved a President's nominee. Liberals made a fuss in each of these occasions because they feared losing the political power the Warren Court's jurisprudence had given them.
See, you're playing around using understandings and definitions of these concepts that weren't really in use before the Warren Court handed down Epperson. What "separation of Church and State" means is not immutably etched into the Constitution. The Warren Court established sweeping, new understandings of this term and several others which 1) should have more naturally be made through the democratic process and 2) put us on the irreparable path to a hyper-politicized the Court.
Can you explain to me how, exactly, teaching creationism would not be "prohibiting the free exercise" of religion? If schools are teaching the doctrines of a particular religion to be factual, then that is clearly promoting one religion, not "free exercise." If the government is funding those schools, then the government is by definition "prohibiting the free exercise." If you want to take it in an originalist direction, it's actually even more clear; many of the men who wrote the Constitution were deists, and they sure as hell weren't interested in the government promoting a religion they felt wasn't entirely true.
All the states in the Union, even the red ones, signed onto the Constitution, and that means they signed onto the first amendment as well, same as blue states signed onto the second. To your point about change coming through the democratic process, if red states are so enamored with teaching falsehoods in school, they are more than welcome to propose a constitutional amendment. Until that happens, though, this is frankly open and shut.
