As I believe I mentioned in the comments for the first one, Nesa's preferred revenge against Hojo involves getting the Finance department given a free hand to do a very wide-ranging audit. If she's really cranky, she adds in the office of Workplace Safety, Shinra Legal, and probably also Shinra IT - she figures if they're cracking down on all the various ways that Hojo can do things illegally, improperly, or with incorrect safeguards against human injury, he's going to be limited to actual biological research performed in a regular fashion, which will quickly expose him as a sham of a scientist.
It's not that she doesn't like Hojo, it's just she thinks he shouldn't have been allowed within a mile of a scalpel.