If you don't understand why it's so wrong to officially validate Rick Warren, read this. Gay kids learn that being gay is wrong, so they try to stop being attracted to the person of the same sex. And they fail. And they have horrible problems until they come to terms with their sexual identity. It's no wonder that gay teens have higher suicide rates than straight teens.
Sexual identity is part of who you are. Period. Passing hate crimes and anti-discrimination statutes and civil unions laws and the like are not bad actions, but the leader of this country announcing that he does not believe that gay people should have the right to marry their life partner, but straight people do, is pretty awful. Saying so while preaching tolerance for bigots doesn't actually change my mind on that point.
America has always had a reactionary streak which reflects other peoples' rights as irrelevant or immoral. There was a morality dressed in Christian garb built up around slavery, denying women the vote and taking land from Native Americans, to pick three obvious examples. But America also has a strong anti-racist tradition, and this tradition does draw power from the line that 'all men are created equal'. Well, um. You get the picture. Anyway, both can create political power, but you can't throw away the rights of one group without damaging the rights of other groups. Gay rights and women's rights advance in legal circles, building on each others' precedents. And I don't think it's a coincidence that America so egregiously kills Iraqis without consequence to its political leaders, and that the same groups that push said decisions (like Rick Warren) are the ones that seek to deny gay people rights.
There is no three dimensional chess here or political calculation that makes sense on this point. If the argument is that sacrificing the rights of another group on the altar of political power is a reasonable choice, then you should remember that a society that callously denies one group their humanity can just as easily deny you yours.