The distinction between these points is important to me, I'm glad you bring it up. I know I've been somewhat contradictory on this, but I'll say I agree that the given joke, as it stands, is not respectful. If it were a guy's gathering, I think it would be ok, but it's an open invitation.
Since I've been saying that the problem is about bad taste in humor, I've been trying to come up with a better way of making the same joke (if we are to take them on their word that this joke was really about being a male dominated field). What do you think of this variation (not to say it's that much more funny):
"Women: Yes, we aim to make a welcoming atmosphere for women who want to participate in our hackathon. (And for those men still afraid of getting out-programmed by a girl, we've hired an all-female event staff to serve you cold beer.)"
Granted it maybe sends a bit of a double-message still, I think something more along these lines could make it clear that we mean no real disrespect, but still keep it from getting too uptight.