In the canon setting of the series Madoka/Homura and Kyouko/Sayaka have strong (romantic) feelings for each other. Note, strong is a term that means something is high in value. In the state of their feelings for be strong for each other they are obviously in love with each other. Seeing as how if you portray the feelings they have as stronger than in canon they will only be even more attracted to each other that means the only other directed the feelings can travel in a crack setting is lower. This means that Madoka/Homura and Kyouko/Sayaka’s feelings are being portrayed as weak in the new crack setting because if they weren't being portrayed as weak they would still be in love with each other rather than their crack setting counter part. And obviously, weak is a term that means low in value. Now, remember what it meant to degrade something? To lower it in value. This is what you have done in your crack setting. You have made their canon feelings be portrayed as weak than what they are for the sake of pairing them without someone else for the sake of amusing yourself.

Of course you as a third party can not actually effect the canon characters to degrade them. What’s being discussed here is that in your personal portrayal of them they have been weakened and degraded. The issue is not that the canon characters have been changed, but that you as a viewer are saying negative things about them. You are saying their feelings are weak in your portrayal of them, thus you are degrading them. It doesn't actually have to effect the characters, it’s similar to insulting someone behind their back. Which means to insult someone without their knowledge of it (thus having no effect).