Perhaps they tried to force him out and he refused. Wells Report and all the so-called witch-hunting came after the SB.
It's easier to tuck away and make Brady the fall guy because if Bellicheat really has been pulling the strings all along, it discredits the last 15 years of professional football, during which time ONE team has been consistently in contention and during which time the brand rose to prominence WELL ahead of any other professional sport in the modern era.
If it comes out that the Patriots* single-handedly (through Bellicheat) compromised the integrity of the last 15 earth shattering, ratings obliterating years, then the NFL stands to lose A LOT.