I think we are reading into his death a little too much. It is clear that Coppola wanted the viewer to doubt the explanation given for Clemenza's death, but with Hagen, I think it is what it is. He died of natural causes, and Michael remains close with his son and wife. As it was brough up before, if Hagen was killed, I think his family would not be as close with the Corleone's as they are.

It would have been so nice if Hagen was in Part 3 so we could see the end of the struggle between them, however, I think that they would have ended up together because Michael had regretted killing Fredo anyways. Unlikely that he would have done anything to Tom, even if provoked.