If they'd addressed objectors with a simple and genuine apology--something along the lines of "we never wanted to trivialize rape, we are sorry"--I'd probably have been okay with that.

Same here. I find the core joke of the comic quite funny, video game logic is absurd and they don't need the rape line to make it funny. If they'd just apologised this never would have escalated the way it has. The whole thing smacks of butthurt incredulity at the idea of people criticising them. It's like they think they're above reproach.