It's apples and oranges. One is a internal human resources issue involving potential hostile work environment (ie discrimination) implications and the other is an allowable business decision that can obviously be judged as poor taste (offensive).
I don't know who has offered up your claim about the singular direction of racism but it's untrue and not really cogent to the issue. I would equally support resignations or terminations of a minority employee of a team or NFL if they wrote such derogatory and hateful things that are easily interpreted as discriminatory. Employees, especially those in leadership positions, shouldn't be allowed to behave in such a way in the workplace. That's true for any individual, without regard to their race, sex, etc.
His resignation was likely self serving given these were communications the NFL was already investigating. A termination was very possible in the near future. It's tough to imagine his bigoted opinions in those communications didn't color his professional interactions with female referees, the NFL itself or minority players in the subgroups he insulted. A smart organization would rid itself of such an employee ASAP as they are a massive liability for any brand and the true integrity of a professional work environment.