I'd suggest that this particular joke isn't very funny or meaningful and in my eyes detracts more from the message than it adds to it.
I wouldn't want to have an offical list of things you can't joke about, but that doesn't mean that all jokes are necessarily funny, and won't make me think less of the person choosing to tell them.
You are issuing the point entirely. Notch is highlighting the fact that Callahan presented a loaded argument: that he only supports open platforms. He then highlights the sheer unfairness of the argument with an absurd and controversial statement of his own: that of goat rape.
That's not a joke, that's a form of argument ad absurdum.
I don't believe the point was missed, the article could still use absurdity without the absurd act being rape. It was distracting to use rape as the absurd action and weakened the message delivery.
I wouldn't want to have an offical list of things you can't joke about, but that doesn't mean that all jokes are necessarily funny, and won't make me think less of the person choosing to tell them.