I think the inappropriateness of "forking one's repo" stems from the way it is phrased. I'd never seen fork applied to a repo before (maybe others have), only to projects, so for example someone might say:
I've forked Linux.
The way they've phrased it, though, is more like:
I've forked Torvald's repo.
Which does sound a lot more sexual, as you can easily imagine repo standing for any "forkable" body part.
Given that telling women that they're fuckable is a widespread sexist "praise" (it equates their value with their sexual desirableness), given that the fired guy considered telling that someone's repo was forkable was a praise, and given the close correspondence between the two idioms, I cannot see how saying it the way they did could not be sexist, though I doubt they were conscious of it.
Furthermore, in the specific case of the fired guy saying:
The sexual context was applied by Adria, and not us.
It is incorrect. Adria said:
He said he would be interested in forking the repo and continuing development.
That would have been fine until the guy next to him […] began making sexual forking jokes.
So she clearly didn't ascribe a sexual innuendo to the original use (though, as shown by the beginning of my post, I think it is there, albeit subconsciously).
What I would like to know is how did they go from "forking someone's repo" to a sexual joke about big dongles without an intermediate step of an overtly sexual forking joke. It's not like forking a project (or a repo) and hardware dongles have anything in common that would link them.
Nothing in this episode warrants anybody losing their job or getting rape and death threat.