Forget the joke for a second, because the problem has moved beyond that. The main issue here is the response to the ensuing escalation. After some people commented on the Sixth Slave comic and how they didn't really think it was appropriate (for the record, some of these people were rape survivors, and they didn't even comment on the PA web site, but their own blogs), there was an armada of "but free speech" complaints and rape and death threats. It could've all died down then and there had Gabe and Tycho just said that the comic did not mean to belittle rape, but comment on the silliness of MMO quests. No, they fanned the flames with a flippant followup strip. And then there was the whole "Team Dickwolves" shirts, and that snowballed. The entire debacle has been fully chronicled here [http://debacle.tumblr.com/post/3041940865/the-pratfall-of-penny-arcade-a-timeline] (page 1 & 2), if anyone wants the hard facts.
Of course, Krahulik posted an apology a few days ago with does seem genuine even though it still says "I'm sorry you were offended" (and not "sorry I offended you", big distinction). However, Krahulik does have a huge track record for putting his foot in his mouth, not just on this issue, but also regarding transgendered individuals. Only time will tell if he's truly changed.
And I'm sorry, this has nothing to do with being "figureheads" and whatnot, this is just about being a decent human being. No one's telling him to "shut up", but to have a care with the language he uses. That's just living in a society, not a vacuum.