I feel like the Patriots/Niners trade was good for New England as well. I used to live in New England and I'll tell you only a superbowl matters to the Patriots, anything less is failure.
Viewing from that perspective, they can't win a superbowl with Garapalo if Brady gets hurt. So why keep him around? They have a good enough record half way through the season to make sure they'll make the playoffs, Garapalo was insurance in case of an early season Brady injury to keep them playoff bound. At this point in the season, with a good record, they're all in with Brady. With Garapalo at the end of his contract, they had no hope of resigning him next year. He wants to start and is good enough to get a better offer from somewhere come the offseason. Might as well get a solid pick for him and salary space, than nothing at all. They've doubled down on Brady staying healthy through the playoffs.