We all know the player's potential is weighing on everyone's opinion (including the team's). I personally say cut him because the charges are pretty serious, he already has a criminal record, and his player conduct history is poor (including with the Patriots in only 1 season).
Kraft is going to consider public opinion and the overall ramifications on the his reputation and that of the team. The Hernandez situation has forever put the team in the position of being extra sensitive about these criminal matters (particularly ones involving guns/weapons). Kraft has his own prior legal issue that he doesn't want conjured up for any reason. There's an overall history here that is not going to be unrelated to this current situation, which I suppose is unfortunate for Jones, but that's just the way it is.
Belichick has got to consider the distraction element on his team's preparation for this very important season. Everyone has to on point this season and this isn't a good start. It's hard to ignore the noise when it's coming from within and it's in your face. Removing the distraction now and moving forward may be the most prudent approach. I get it - innocent until proven guilty - but that's in a court of law and it will be dragged out and scrutinized for months. In the meantime, people (and the court of public opinion) will be passing judgment on the player, the team, the HC/GM, and ownership. So maybe it's soft in some respect but cutting the player now could potentially avoid a lot of grief.