I'm always a 'keep your god damned hands off comedy' sort of guy, but there is certainly a lot of nuance to this. When you're in public space, or someone else's space, you have a lot of reason to to be polite and tactful. When you create your own space, (like Penny Arcade), is it appropriate to get offended about a single rape related comic in a series that has a (as often pointed out) literal rapist? Was the comic 'wrong'? No, the comic wasn't wrong and Mike and Jerry did nothing wrong (yet), but the outrage was probably a net good. Awareness needs to be brought to issues and you don't bring awareness to issues by going "Haha, that was funny guys, but remember, real people get raped and real people are rape survivors". The controversy got people to read and argue things.
Mike and Jerry to an extent are victims (however small) of social injustice too. While comedy naturally tries to make fun of everything, social injustice is always going to cause backlashes against it. In this cause, feminists HAVE to get upset about things and they HAVE to push. Again, you don't tip toe quality toward equality. By necessity 'they' have to overreach and the social mechanism for this is the loudest fringe groups that get the outrage started.
The real problem with social injustice with things like rape, sexism and racism is a lack of proper awareness. For example, I really liked Rapelay. That game was great. When the controversy broke out with it, I had to ask my self... Is this game sexist? Is it bad? Is it wrong to like it? My thinking on the matter is yes, it's sexist. But that's not necessarily bad. Most FPSs are sociopathic, but that's also okay. It's also not bad for me to like rapelay because I KNOW WHAT IT IS. I can call a spade a spade. It's a horribly sexist game and thats WHY it's fun. The problem is with issues like sexism or rape, awareness is low. Pretty much everyone can play a violent video game and go "Yes. This isn't reality". Hell, I'd say most people could, if it was their bag, play a game like rapelay without any issues. It's so blatently sexist that it's easy to brush off. But "most people" is not a good answer. It needs to be much closer to "all" people and when issues are more subtle, it draws closer toward 'almost no people and then we get things like unintentional sexism in games and other situations and the whole thing is a mess and it sucks for everyone involved. Of course, women suffer by faaaaar the most, but still, everyone is still somewhat victimized. I wanna be able to play games like rapelay and throw around gendered insults in appropriate spaces without being hassled and for that, people have to see what the hell is wrong with society.
So yeah, part of me hates seeing comedy shamed, but this stuff has to happen and honestly, if anything is going to generate the most awareness with the least amount of harm the the original authors, it's going to be Penny Arcade. The sooner we get everyone on the same level, the sooner we can get back to being vile without having to be nagged all the time.