The problem is the swing states, which are critical for winning obviously. Many of these swing states, NC being one of them, are generally opposed to same sex marriage. Think about that 61% of voters in NC that Obama probably angered with this. I think this is why he has been so reluctant to take any stand on the issue, he has kept the water muddy for a reason. Thanks to Biden though, the press and his base had basically forced his hand. By pleasing his base, he may lose ground in the states that matter.
I can see folks like Karl Rove going to NC and other swing states and using this to attack Obama there and damage popularity, he basically gave them ammo.