The reasoning isn't crazy. It's technically correct. If you're being true to the idea that government must not take positions on religious questions, then the Ninth Circuit opinion is quite persuasive.

Today the world faces a single man armed with weapons of mass destruction, manifesting an aggressive, bullying attitude, who may well plunge the world into chaos and bloodshed if he miscalculates. This person, belligerent, arrogant, and sure of himself, truly is the most dangerous person on Earth. The problem is that his name is George W. Bush, and he is our president.

Every religion I know of has changed its views with respect to concrete controversies over long periods of time. People's views about the morality of homosexuality are likely to undergo some change, even though they're making judgments based on their religious beliefs. Because in fact, religion is an extremely durable, and yet flexible, way of trying to apprehend what's good and what's bad in the world. In fact, its durability comes from its flexibility. Now, speaking from inside a religion, it's hard to talk that way.

There is a powerful desire by majorities to assert a religious identity for the country.

The reasoning isn't crazy. It's technically correct. If you're being true to the idea that government must not take positions on religious questions, then the Ninth Circuit opinion is quite persuasive.