We can sum up the situation well if we conclude that it's Milan who went way over the line and despite being a Juve fan I am saying this without any bias at all.
First of all, Milan were badly damaged with that disallowed goal. But if they are objective they will admit that it had nothing to do with Juventus and all to do with the incompetence of the linesman. That same linesman disallowed a Matri goal in the 79th minute when the result was 1:0 for Milan. He 100% wasn't gonna disallow the goal so late into the game if his intention was to help Juve not to lose.
Milan players did lose their minds. They worked really hard for a win and then a simple ref decision ruins so much of that work. That's why the happenings during and immediately after the game can be somehow excused. Mexes' punch, Muntari's punch, Galliani's reaction at halftime and Ambrosini's post-match attack on Chiellini.
What can't be excused though is how they went gun blazing on Juventus. As if it was Juve's fault that the linesman disallowed the goal. Juve weren't getting any help through out the season and Milan had no recent history to call in help in order to excuse their reactions. The Pirlo video was pathetic. Publicly announcing how we "aren't friends" anymore was pathetic. Just as pathetic as FIGCs handling of the situation.
The good thing in all this is that Galliani realized his mistakes and, rightfully, he was the one who called Juve to apologize, because it was him and his team that attacked Juventus for absolutely no reason.