I feel Barristan, both in the books and so far in the series, has been more of a Hand than a mere queensguard to Dany. Aerys had plenty of people in his court, and he was a young knight among many, while Dany is a green queen surrounded by strangers. Sure, in the books he doesn't usually say what's in his mind without being asked to, but it doesn't strike me as too out-of-character his shock to Dany's trade of a dragon.
I think at this point in time the Boltons are still loyal Stark men, or at least loyal to the cause of the North. I don't remember quite well how premeditated Roose's betrayal was in the books, but I don't think so far in the show he's even cogitated an alliance with Tywin. I don't even think he plans on using Jaime as a hostage, given his talk of revenge with Karstark in 3x01. Matters little the state of a man marked for the axe, so long as he's alive.