If you go to the Sopranos HBO website, the episode recap says that she died of a stroke.

I do believe that the writers tried to make Tony look like a villain in season 6 part 2 - if anything, so that people would realize how awful gangsters are and would root for some sort of comeuppance. But I think the "villainization" here is the fear of being killed by Hesh and Tony's harsh behavior and crude remarks behind Hesh's back. Tony forgot about that Ojibwe saying - "Sometimes I go about in pity for myself, and all the while, a great wind carries me across the sky."