Imagine that I'm a pal who explained the modern analogous position to you. I tell you that I think our prisons are inhumane, and the death penalty is problematic. I know a guy who beat up 3 cops, a teacher and some kids and drugged them so they forgot what happened when they interrupted him slaughtering some horses, but I don't report him, and in fact helped him cover up his crimes because of my belief. We still buds?

You confuse agreement about moral principles with the judgement that a moral system is consistent. There are a lot of possible ethical systems that I don't like. That doesn't mean they aren't consistent ethical systems.

Let's say I know a homosexual from a country where it's illegal with the death penalty. He was in a situation where 3 cops witnessed him engage in an homosexual act. He managed to make them temporarily unconscious and drug them up to forget that they found him.

Would I let that person get away with that? Probably yes. How I treat someone who opposes a cop depends a lot on whether I believe in the law of the land of that cop.

Suffering is certainly bad, but Harry's cool with False Memory charms, and those can negate suffering.

I don't think there's evidence to the claim that false memory charms can negate all suffering.

Not only that, he's going to resurrect Hermione, who is dead and whose body is gone presumably by now decayed.

I don't think it decayes in the transformed form.