I think everybody gets along with JM. The fact that most, if not all former players speak highly of him suggests as much.
The only known public disagreement that I know of was with Roman.
Of course you have had the Mario and Adriano thing, but he has seemed to make a mends.
As for Baresi, I see no evidence that they don't get along, JM seems like he wouldn't tolerate somebody around him, that he didn't get along with.
This could also be public persona, the public thinks that JM is not very socialable, but I would say from his Italian interviews and from what I've seen from various media sources, he a very fun guy to be around...however as the poster above has said, who knows?
Baresi was in charge of the side when JM was suspended, if I'm not mistaken, that speaks volumes.