People don't want to accept that it became a binary choice between Brady and Belichick at that point. It wasn't a situation where Kraft could tell Belichick to keep Tom and treat him differently. Tom was no longer tolerating Bill's treatment. He wasn't going to stay unless significant changes were made to how Bill ran the team.
Kraft went with the coach who just won a defensively driven Super Bowl who in theory should have had a longer shelf life, than the QB in his 40's. It wasn't some crazy decision either. Brady realistically played well for about 2 more years and fell off in the third (though not bad enough that he absolutely had to retire). What was unexpected, and most of this fanbase would likely acknowledge, is that the mythologizing about Bill Belichick and his magic system fell apart as soon as Brady left and he turned back into the guy from Cleveland and the team progressively got worse until his tenure was untenable.
But at the end of the day it came down to a choice and Belichick was the safer choice. Even if everything on the Brady end went exactly the same, nobody expected Bill Belichick to tank the way he did and look completely incompetent and hire goons like Patricia.