Family or not... the same way you wouldn't always agree with what your own blood relatives do, maybe Thought didn't agree with backing up Jay-Z on television. Maybe he thought too that it would be a contradiction and decided to leave that one alone. It's one thing to be "cool" with Jay in person, but he knew how it would look if he got on the mic with him.
Bottom line, you don't always agree with your "family" on things so I don't have a problem with Thought as far as that's concerned.
I didn't agree with how he pointed the finger to the video director, because like you said, he "was there". But although he made it clear that The Roots is his family, he probably just didn't agree with one of their business moves. Period.