I wrote up a fairly length response to ProfessorCirno, but then I closed it by accident when I went to eat some raisins so I'll boil down the main points:
First off, the problem was never with the first strip. Ok someone got offended and wrote up a big thing about it, so what. It's not the first time someone got pissed at PA.
But, barring one other incident how many years ago, it was the first time PA felt to respond with another strip mocking them for it. And then to merchandise it. You could've just ignored it. You could've said "Whoh we didn't mean to make fun of rape folks." You could've even just gone "Look we're Penny Arcade we make rape jokes." Instead you decided to mock a goddamn rape victim.
This, and the paragraph or two that follow, are broadly right, I think. Mike and Jerry clearly misunderstand the objection, and have thus mocked these people in a way they definitely don't deserve to be mocked. If that was the entirety of the issue, then I'd agree with you that PA is definitely in the wrong on this thing. It's not, though, and you realize that:
In today's internet culture, rape jokes are everywhere. Play an online game and read about how much people are raping you, how "you gon' get raped" if you walk outside alone, how much she was asking for it - a sickening defense still used in courtrooms. Bizarrely enough, you'll find that rape survivors don't find this funny.
So really the problem isn't just Mike and Jerry's rather blunt response: it's rape jokes in general, like the original comic that you said was fine. The point that I had made in a few paragraphs before but that I will now simply sum up is that if we carry the most reasonable arguments from both sides through to their conclusions, I think we come out on Penny Arcade's side and specifically on the side of the Dickwolf shirt.
People who take umbrage at the shirt and at the strip (but not at the strip where the Fruit Fucker molests Tycho's wife, or the one where Tycho is going to be raped by the TSA, or the customer raping robot) are, when you get down to it, one of the many people who form their own contingent of the joke police, a cadre that roams around the world telling humorists what it isn't okay to joke about. Rape is probably the most popular topic, followed by race, religion, sexism, and so on, but the sentiment is in my mind indefensible, especially
when we come to rape, where the stigma is so big that many people feel completely unable to share their experiences or even report the rape.
Telling people that rape is so horrible that we can't even make jokes about it, even when we make jokes about genocide or torture or dead babies or whatever, is telling them that if they've been raped, they're never going to get over it, or at very least they'll never be able to make light of it.