It's not the discrimination that makes them look bad, it's the having it acknowledged openly and in those exact words.
Look, everyone knows that most news media outlets in America are in the bag for the DNC. It is one of the most blindingly obvious things in the world. But look at how hard they fight to avoid admitting that or being called on it. They will deny to their graves that they are biased and have an agenda. In their eyes it doesn't matter that everyone knows they're biased and have an agenda, because as long as they lay claim to objectivity they have it. They're big on the power of labels, after all, so as long as they can claim they're objective, to them they have the respectability that's associated with objectivity. Admitting to their bias would take away the label though.
That's why Marvel would be likely to distance themselves from Waid, say "He doesn't speak for us", and stop hiring him. It's not that he persecuted conservatives, or made conservatives mad, it's that he admitted to the open secret and damaged the veneer of the narrative.