Note that I set the poll so you can choose more than one option.
Finally, here's a recent article from Wired magazine that sums up the whole debate (admittedly from a point of view that's critical of Penny Arcade and Mike Krahulik in particular):
My personal opinion is that the original comic was actually pretty funny. It didn't seem to be making light of rape exactly, it was more a play on the absurdity of MMORPGs that don't give you a reason to care (or even the option to care) about the "6th prisoner" in a quest that only asks for 5 prisoners, which is kind of a jarring break from the fiction of you playing a hero out to help people.
However, Mike's subsequent responses to criticism were really tone deaf and completely unempathetic, and he made the choice to double down on this stance when Penny Arcade released the dick-wolf shirts in the store (Mike went on to display the same kind of attitude when a debate over transgender representations came up).
Recently Mike made a comment that he wished they hadn't taken down those shirts from the store, which is why the whole debate is being dragged up again.
I really think that this would have gone away if the original response to critics of the comic was "oh, I understand where you're coming from, we didn't mean it to be hurtful", or even just saying nothing at all.