What do you think happened with the Rosato Brothers? Do you think Michael would've had them killed, or made peace with them?

The last thing we heard of them was at the end of Part II when Tom said that they 'were on the run'. But in the beginning of Part II Michael was even defending them against Pentangeli stating that Frank had denied them Clemenza's promises. He even withheld Pentangeli from killing them.

Couldn't it be that the Rosatos only held a beef against Pentangeli and not Michael? Weren't they manipulated by Roth?

I think the Rosatos would've been capable leaders, but I think they were too ambitious for Michael to control them. Still, I think there's a very slim change they could have taken over from Pentangeli. But by the time of Part III we didn't hear about them which implies they were out of the picture.