I think that what race control said pretty much sums it up....
MM didn't make contact, and didn't break any "rules", but was riding in a way that (intentionally) caused problems for Rossi. Rossi reacted, but unfortunately reacted in a way that is against the rules.
BOTH riders were at fault for this incident, but I think the 3 point docking of points is fair because Rossi could have very easily have finished 4th, instead of 3rd, IF MM does not go down. MM needs to be reprimanded and told if this happens in the last race he will be black flagged and fined.
Things like this are not good for anybody involved.