I know that there are other such phrases that offend people. I've heard pushback with regards to "trail of tears" and "death march." And, of course, if you use "lynch" or "lynching" to refer to anything other than the extra-judicial execution of a person, for a perceived crime, by a mob, then you're just asking to get called out (or 'called in' as my friends are saying now).
I've never heard of anyone taking offense to 'witch hunt,' and my hasty googling revealed nothing, but it's certainly something that a person could, conceivably, find offensive. Like, the world has witches. They often perceive themselves to be a persecuted religious minority. Talking about how there's "The internet is staging a witch hunt to find people who misuse the term 'witch hunt,'" might possibly be very offensive to someone.
I think that all these social justice conversations don't really work unless you believe people about the depth and enormity of their pain. Sometimes it's hard for me to do that, since I'm only really offended by terms that are already consensus not-okay. For instance, calling something "gay." Offensive. But the number of times I've heard someone say that since becoming an adult is very small. I'm not really on the cutting edge of taking offense at terms. But I do make an effort to believe people. So if someone were to chime in and be like. "never say 'witch hunt' ever again!" then I would probably make an attempt. There'd have to be a few reminders, though. I've been trying for years to stop saying 'lame' and have yet to quite manage it. If once in my life someone in real life had been like, "Rahul, it really hurts me when you say that," then the experience probably would've been so scarring that I'd have never said it again. But since at the moment this is a taboo that, for me, exists only as a result of conversation on the Internet, there's something vaguely unreal about it.
Although, actually, maybe I don't say 'lame' on the internet? At least I'm not seeing any hits for it on my blog. So maybe there's a certain amount of code-switching going on. I don't say the word on the internet, where I know there's a chance someone will give me shit for it, even though I do say it in real life.