You have to stand up to the trolls now. The internet has created a permanent record of slander and humiliation from anonymous people, so if you don't stand up to it then it'll be assumed that there was some merit to what they said.
If Zed's story is correct, an it'd be foolish of him to have claimed this it if wasn't, then this particular individual is proof that ignoring trolls doesn't work.
There's also another problem with your response - why the hell should anyone _else_ have to deal with unwanted dickjokes? Github almost certainly don't like the way Zed's brought attention to this, but it's _their_ poorly though out infrastructure (or more optimistically, their incomplete implementation of a good idea) that's providing a platform for Nick to go round harassing people he doesn't like. Nick needs to grow the fuck up and understand that unwanted dickjoking and homophobia isn't funny outside his special little circle of friends, but Github need to understand there's millions of idiot-Nicks out there, and ensure their product doesn't even allow this sort of behaviour to start.
I wouldn't necessarily fault github in this situation. The product started with a great community and it would have been wasteful for them to have spent their time early on implementing defense mechanisms against abuse instead of focusing on features.
For example, I wouldn't expect them to add spam filtering to their message system, but if viagra ads started popping up on github it'd be a worthwhile addition. However, to label that poorly thought out or an incomplete implementation of messaging seems unfair.
Of course, now that the community is larger and github is being used as a platform for childish squabbles/recruiters/etc, it's a good idea for them to fix these types of issues as they pop up (which they're already doing).
Yeah, I guess that's where I was going with my "incomplete implementation" alternative.
Sure, you launch with a MVP that doesn't include protection against trolls, but you really want to have at least a plan for how you're going to deal with them when you finally gain enough traction to start attracting them (and if _I_ were Github, I'd be profusely apologising to Zed, and _very_ publicly smacking down Nick (and his idiot copycat friends)).