This all tells me that Belichick was, at some point, looking at the long-term... as in, "yeah - I want to continue coaching, and I don't want to be left with nothing to work with as far as a replacement at QB."
I think Belichick would've rather let go of Brady than Garoppolo, and given Tom's age - it would be understandable. Bill knew how talented Garoppolo was, he scouted him and drafted him. And he was learning from the best while he was in NE, so it was just a matter of when, not if.
And Bill also has a reputation for not being fond of developing young players, especially young players these days with all of the emotional baggage and off-field problems that some bring with them. He is very much old-school, which is why he's become a jack-of-all-trades as it pertains to free agency acquisitions.
He's not looking for drama. He wants yes-men, guys who show up on time, guys who don't question his authority, guys who don't give him headaches as far as distractions go.
Which, imo, is why the thought of him taking a job in NY (imo) wouldn't appeal to him. Too many drama divas on that team, not to mention that he'd be inheriting a similar situation there with regard to an aging QB whose skills are deteriorating, and no real future at that position for the immediate future.
The question isn't has Kraft lost confidence in Belichick, but has the coach lost confidence in his owner? And how much longer is Bill looking to coach under that situation? Brady will likely be there for at least another year or two. Of course - they can make it work, but it'll definitely be different.