Changing GMs is like changing who lives in a house when you've already ripped up half the carpet. The new occupants have a different idea of what to replace that carpet with, and what to do with what remains.
The cause in the NFL for any team is to win, or at least do better. With the season lost, there's some compromise made to save $$ where possible, especially when it is as substantial as Quinn's bonus.
In 2-months to a year maybe we'll find out more about this situation when Mangini is out of a job and finally talking frankly about this season.