It's seemed all along that Malcolm did something, and that there will be rumors and innuendo about it, but that ultimately regardless of what it was, it wasn't bad enough for the team to completely exile him, and they have no desire to harm his free agent prospects (both because that's a bad look for future players looking to join up with the Pats, and because he's likely to go to a contender and it's counter to their interests to depress his market).
OF COURSE Butler did something and Belichick is lying about it. Of course the media are going to dig around and try to come up with the most sensational-sounding explanation. But if the Pats don't leak, no one rumor is likely to gain particular traction, and the whole thing will basically blow over for Belichick. There's a discussion to be made, in terms of how good you think their prospects of future SBs are, that it might have been better for BB to ignore his rules and just make the short-term move to win the game, given how high-leverage the single game was.
But no one who's witnessed a moment of how Bill Belichick operates will be surprised. Even if it's hubristic to think they will make it to another Super Bowl, it's the kind of hubris that's necessary to succeed in top-level sports. It's frankly insane to punish players for being late to practice during a snowstorm, but forty-five of the guys on that roster knew it was going to happen and made it in on time anyway. Belichick's way of doing things relies on engendering that level of fanatical commitment in everyone.