Hm. Interestingly Wikipedia defines the term differently than I expected:

In current language, “witch-hunt” metaphorically means an investigation that is usually conducted with much publicity, supposedly to uncover subversive activity, disloyalty, and so on, but with the real purpose of harming opponents. It can also involve elements of moral panic, as well as mass hysteria.

By that definition you can indeed call it a witch hunt. But somehow it still feels wrong to call an investigation a witch hunt, if the person being investigated really did commit a crime.