The problem with the joke is that it's rooted in sexism. You see this a lot in male-dominated fandoms: every time there's a powerful female leader who isn't portrayed as an evil dictator in canon, male fans will inevitably characterize her as secretly evil and manipulative. Sometimes as a joke, sometimes seriously.

And I've seen plenty of Bronies who actually take the whole "Celestia is evil" thing seriously, mostly because she imprisoned her sister for 1000 years. You know, her sister who had turned evil and was never going to let the sun rise again. Yeah.