You're somewhat missing the point. Yes, everyone knows it was a joke. It was a joke that could have gotten someone assaulted. People aren't just following the letter of the law, here. This is a thing that happens for good reason.

A normal person who pulled this sort of prank might not get noticed and have this happen to them, but they shouldn't be surprised- threats to public figures, especially women, especially politicians, are serious business. A normal person is likely to get away with that sort of crap because no one who cares would notice, so they get a bit of leeway that people with thousands of social media followers don't. Such is the way of things.

Someone of Shkreli's wealth would also, ordinarily, not go to jail for it, because the wealthy can hire powerful lawyers and generally work the system. It sounds entirely plausible, from the article, that personal dislike had a prominent role in the judge's decision. But then, I can't feel sad Shrekli's status as a nationally-reknowned sociopath balances out his wealth in this case. Such is also the way of things.