I don't know him, nor do I have any reason or desire to defend Alex Guerrero. This post might be taken that way, but I can't do anything about that, so here goes...:
There seems to be as many anecdotal stories of TB12 helping players and laypeople alike as their are critical ones, not least of which is Tom Brady himself. With Guerrero's help, Brady has started 196 games since 2009 (in other words, every game allowable plus playoffs since the season following him beginning work with Guerrero) and has extended his prime more than a half decade beyond the retirement age, let alone effectiveness, of other recent Hall of Fame quarterbacks.
Player Age - end of prime/retirement
Marino 36/38
Montana 34/38
Troy Aikman 34/34 (Suffered a concussion as a result of a nasty LaVar Arrington hit, but maintains he retired due to because of back pain after the Cowboys released him.)
Steve Young 37/38
John Elway 37/38
Peyton Manning 37/39
At the end of the day, the TB12 method combines the principles of the Mediterranean Diet, massage therapy, and principles of pilates/yoga/stretching, and mental well being over heavy-weight training. Another player who uses alternative health maintenance in retirement is Brett Favre (40...argument can be made for 36/36, 37, 38, 39, 40, and 41) with his copper fit compression clothing. It seems reasonable to at least consider exploring alternative health practices, in the face of where healthcare "insurance" costs are, seem to be going, and pumping one's body with pharmaceutical after pharmaceutical to treat side effects of other pharmaceuticals.
Now to answer the question at hand...I think Brady wants to stay with the Patriots, and based purely on my own entertainment factor, I hope he either re-ups or retires. OTOH Belichick has a history of being unemotional with his philosophy of cutting players loose a year before they lose effectiveness than a year later. To which I say sign Brady for 2 years, and draft a QB at 23 or 2nd round.