Ok, I kind of thought a few minutes after pressing "post" that the Matthew Shepard reference would be distracting. So let's set that aside for now. But allow me to go further on two points:
First, if there were a video of simply a girl punching a guy in the balls, without any further context, that would not be funny. That would still be dumb. Even accepting, for the sake of argument, your premise of gender blindness (i.e., it wouldn't matter if this were a girl doing it to a guy, or a guy doing it to a guy, or a girl doing it to a girl), it's still just a video of one person doing a violent thing to another person. That's not funny; that's just some empty internet video, of the type very intelligently lampooned by Human Giant here:
http://www.funnyordie.com/videos/d6e1037cc2.
I agree that the concept is ridiculous enough to be funny in a sketch or improv scene, under any number of different scenarios you've shared with, and thus established with, your audience (e.g., the guy is an unorthodox OB-GYN; or the woman is demanding it as some part of S&M play; or she is an alien robo-zombie whose entire body is made of impenetrable steel machinery, other than her one still-humanly-vulnerable Achillean part). Or this would even be funny, on some level, if you knew that the guy was, I don't know, Sean Penn or Russell Crowe, and the woman was a freelance photographer, because you'd have the added information and context of celebrity privilege vs. the intrusiveness of the paparazzi. But random person punching random person in the crotch? There's no cleverness, no insight, no game. We might as well be watching videos of people slipping on a banana peel. In any case, I think you agree, to some extent, since you point out that the video was "the same 30 seconds of silent, black and white footage replayed over the span of 2 minutes."
Second, I don't think we can ignore the social dimensions of something; that often has a TON to do with why something is funny. I don't know if on paper this makes me less committed to the idea of "gender equality," but when presented with the premise "man hits woman," there's a whole lot of cultural baggage and information that gets conjured up with that (e.g. domestic violence/ingrained machismo), all of which points generally toward that being a particularly undesirable, and wrong, thing. Now I'm not saying that therefore the premise "man hits woman" should never appear in comedy; rather, I'm suggesting that, in order for it to work, that additional information as to the cultural meaning of that interaction should be used and can provide the context for a very funny scene. In other words, we can't really ignore that something like "man hits woman" is taboo (and for good reasons, I'll editorialize), and we should be aware of that in approaching how to use that to get to the funny. The premise "woman hits man," on the other hand, has a different cultural meaning; one that, I would submit, already has a built-in irony -- given the association we have, however unfortunately for gender equality, that it is typically the other way around.
