I'm in the same situation. I love the Cowboys at home on Thanksgiving against a favorable throwing defense. What I don't love is that the Cowboys O-line is decimated. The only problem is there is no time to make this call you have to commit by Thursday. There is still an outside shot that Alex Smith gets cleared to play so picking up Kaepernick could end up in Smith starting and potentially some kind of QB time share.
As of right now I'm sticking with Romo. He got sacked 7 times last week and still got close to his projected Yahoo score.