I've always wondered about that one too. I mean naming is a minefield, but using a name that's well known to be at least mildly offensive in a particular dialect of English is probably something I would have chosen to avoid. I suppose at least they didn't call it "prck", "twt", or "cnt". One has to be grateful for small mercies.
I think you'd get different answers from different people but you can really put your back into the UK pronunciation of "twat" to make it sound really venomous, as opposed to the much more innocuous "twot" pronunciation of the US. That tends to make it more offensive. "Git" just doesn't have quite the same impact.
From what I recall it was intentional on part of the early git team. They did want to make it clear it was a "dumb" VCS compared to work going on in some of the smarter ones such as darcs. git has always had something of the Unix "worse is better" philosophy at its core, and it is amusing it chose to wear that so much on its sleeve that it took that as a name.