I feel like BB did the best he could to manage the JG affair. If Jimmy hadn't gotten hurt in that Miami game 2 years ago and the world could have seem him for 4 games, we'd have gotten a lot more. The Pats held him as long as possible in the event that Brady either got injured, his play declined, or he had a change of heart about retiring.
Finally BB had to either trade JG, cut Brady, or get nothing in return. He went for the high 2nd plus Hoyer (a very underrated part of the deal given it was mid-year). Done, move on. Everyone expected it to be about pick 37 not 43, but JG went out and won 5 in a row, no way to forecast that.
Kraft didn't force the trade, but did say that Brady deserved to continue on as long as he can keep playing like this - ergo don't cut/trade TB in favor of JG. There was no way to keep both, no matter what you offered JG, as he would have refused to report next season. He was ready to be a starter, obviously.