The kicker is that even if people downplay it, EVO is still the largest fighting game event out there, to the point where many big Fighting Game releases are announced them a-la Quakecon and Blitzcon. There's still a good amount of "Validation" people can get from Evo, such as with Melee all those years ago (which also was a year Skullgirls almost got in, but wasn't able to thanks to Injustice basically buying the spot over). Because Skullgirls is basically a wide and diverse community, removing it from EVO doesn't hurt the community. as much as it ruins publicity.
On the other side, Skullgirls doesn't need EVO at all to exist. There's many other events that can, will, and already has hosted them, such as Combo Breaker. The significance of EVO is basically that it's shining a rare spotlight on the game that it would usually not get due to the nature of this new Online EVO, and people are feeling that major-burn of the idea of losing that spot thanks to Mike Z's horrid comment. To make it worse, Mike Z basically is the face of the series and also the man who's behind the development of it as well. It's hard to kick him off the company/game, and if they do, who knows where future Dev stuff for Skullgirls will go (or if Lab Zero would even make anything else in the fighting game market)