I think we just have different views on how to approach bigotry. We both can agree that it is a black mark on our society and we should overcome it as a culture.
However, where we disagree is how to do it. I see the current climate of "preventing the spread of bigoted ideas" as creating what we know as the alt-right. If you check 4chan's /pol/, you will see an incredible amount of people admit to becoming alt-right because "so many snowflakes are always so offended and call me names". If, however, we as a society can more tolerate dark humor and bigoted comments, the bigots either stop talking or evolve to accept more tolerant views. This article as whole is perfect fuel for the alt-right to say "liberals are trying to control everything, even jokes".
To your second point: Pepe wearing a Nazi uniform is not dark comedy. It's racism. They're using memes to further their own ideology, as opposed to the Harvard students who were simply making fun of the offensive nature of the jokes.
Thirdly, I truly don't care for whether or not it's high or low humor. All I'm looking at is intent and whether or not an individual is actively desiring to inflict damage on another group of people. Alt-right memes do this, while the Harvard kids would be the first to admit they were simply making jokes who were not hurting anyone other than the people who decided to be offended by them.