Maybe, but it could also be calculated: "If we don't apologize, the mob will cry for our blood even more, and we obviously can't do a non-apology apology, because they'd hate us for that too. Just be humble and supplicate to them so we can keep our IPO--I mean reputation intact."
The apology could be interpreted in a lot of ways. It could be we fucked up and we are sorry. Or it could be, Julie really blew things out of proportion/overreacted/misinterpreted things and we wish we were better able to react to her hysteria, and we apologize for not being able to.
GitHub is a business and they aren't dumb enough to not consult one or more lawyers before releasing their statement. If they are in the wrong, I would have to imagine their best play would be to compensate Julie behind the scene and have her formally come out and say GitHub is doing everything they can to ensure this doesn't happen again.