I agree with the majority of your thoughts, with the one area that I respectfully disagree being that it was strictly football related. In my opinion, any possibility of retaining Jones went out the window when he decided to go out and party during the most important (at the time--divisional round) week of the season. Hell, he didn't "just" party, but he overdosed in some capacity, showed up shirtless and barefoot at the police dept, and made national sports headlines for his actions. It may have been simply too much to look past when attempting to assess the kind of major money that one would with a new long term deal.
I don't know if some of the concern may have been drug use, immaturity, or both--but I would have to think that at least had something to do with the decision. Obviously, that's just my personal opinion, as you may be much closer to being correct than me, but it's hard for me to imagine Belichick not taking that into account.