Then you have to explain how hers went up against Obama. Remember, he did the same thing just to a much lesser extent. He went way softer on her because he worried about the damage to the party. Trump being Trump and also not a Democrat meant he had no worries of anything other than winning.
I think you are right in that negative partisanship has increased. Right now being in politics makes you radioactive on a national stage.
Clinton remained popular among democrats, it was Republicans that were primarily responsible for her loss of popularity in both cases. As soon as they saw her as an electoral threat they hated her. In the middle she wasn't a threat and they went back to liking her. She became a threat again and they went back to hating her.
Watch Obama's popularity rise once he is out of office.