I doubt it's discipline, no offense to Ty. Belichick might've benched Wes for one series b/c of the foot comments - which I think was a huge mistake - because he felt it was best for the team to set that precedent.
But overall, Belichick has a high threshold for judgement when weighing those softer issues (discipline) versus production on the field. We went out and traded for a pretty questionable character in Haynesworth last season, who did some pretty iffy things on and off the field. Belichick weighed those issues vs. his potential upside as a player, and felt the production would be more important.
So, I doubt, suddenly he's benching Wes because of something internal. We've gone over this in several threads - there's a lot going on here that is factoring in, and you can't make one general assumption. A changing offense with a new scheme, new emphasis, new plays; an offense that loses arguably its best weapon in the second series of the game - I mean, there's just too many moving parts.