It was reported by Adam Schefter back in May that the NFL asked the Pats to suspend to two employees and he capitulated. "NFL asked Pats to suspend them prior to discipline being handed down, per a league source in New York,"
Schefter wrote. "New England obliged with the NFL's request."
Also,
From the NFL's release announcing the Pats punishment (emphasis mine): "Patriots owner Robert Kraft advised Commissioner Roger Goodell last week that Patriots employees John Jastremski and James McNally have been indefinitely suspended without pay by the club,
effective on May 6th. Neither of these individuals may be reinstated without the prior approval of NFL Executive Vice President of Football Operations Troy Vincent."
http://www.cbssports.com/nfl/eye-on...spended-deflategate-employees-at-nfls-request
Mr. Kraft will probably reinstate them if he could and he remarks about regretting putting his faith in the League may encompass this as well. Speculation on my part but I think Mr. Kraft did all these things the League asked...suspend the employees; accept the fine and taking of draft picks; etc. in hopes that it would bode well for his QB.