If I see a company engaging in any discriminatory activity, I have a reason to suspect that sort of discriminatory attitude runs rampant throughout the company right through the executive offices.
In this case discrimination means a company that is willing to put on events to help women participate more in a community where they are the minority and face unique difficulties because of that. This kind of choice for Github doesn't harm men, men are still the dominant group and will continue to be so even after this workshop is over.