Obama's decision also reflects a certain view of liberalism. Classical liberalism was concerned with the freedom to hold and practice beliefs at odds with a public consensus. Modern liberalism uses the power of the state to impose liberal values on institutions it regards as backward. It is the difference between pluralism and anti-clericalism.
I don't know that this can necessarily be cast as "anti-clericalism," and I certainly reject the provocative claim that "the war on religion is now formally declared." This is, however, indicative of this shift in American conceptions of liberalism that I referenced last night, away from the idea of non-intrusive freedom that dominated, at the very least, in the antebellum period and toward a new idea of government sponsored, socially mandated positive pluralism. It is no longer enough to merely not infringe upon the life and liberty of another; in fact, infringing on that liberty can be seen as a moral good provide it is done in the service of securing an increasingly bloated list of rights on behalf of another. (Imagine suggesting to an American two hundred years ago--or one hundred, or fifty, or twenty--that abortion, sterilization, and birth control were inalienable human rights that trumped religious liberty.) There does some to be a clash in cultures occurring here--though again, not some vague war on religion--which no longer sees conscience as the liberty so essential that it became enshrined in the very first amendment to the Constitution, but instead considers it to be a private peccadillo to be tolerated so long as it doesn't interfere with the liberated mindset of post-sexual revolution America.
Without climbing too high onto my soapbox, I'd like to suggest that this viewpoint is only possible because of the trivial way contemporary Christians have handled their faith, allowing it to become more about politics than piety, more about sexual ethics than kingdom ethics. I am ultimately convicted that if Christians were to take faith in Christ as the all-consuming, life-transforming, community-constituting reality that it is and allowed it to distinguish us from society at large rather than trying to conform it to social expectations, perhaps it would be harder for the world to see faith as secondary in importance to the all-powerful right to have a thin, lubricated layer of latex between you and the sexual partner of your choice.