The character I love most in the movies is Tom Hagen and I think everything depends on him in this scenario.

Can he convince Neri/Rocco who was truly behind the hit? Main problem for that was the fact that Hagen wasn't the true consiglieri anymore. Or did Michael deliberately take Hagen out of the equasion just to make sure he can handle the family (because he can figure out what truly happenend on who's orders) if he's gone (read: dead) for some reason.

I believe Hagen was capable of doing that. With his dimplomacy skills he is able to talk to Neri and Rocco. And when they are on his site they can also use Pentangeli and a war will be on. After a while things settle down and there will be some kind of truce.