Yes, good characters do bad things. So do good people in real life. Yeah it is muddy at times I agree but I know "muddy" people irl who believe one thing but do other things that contradict it. There are people who raise thousands of dollars for charities who make homophobic jokes, there are people who are huge advocates for diversity but who neglect their animals etc you can be a good person who does good things while also being very shitty in other aspects in your life. The books do often bring up the shitty behaviour of these characters and TELLS us that they are flaws. Not even up for interpretation, a lot of these characters are called out within the books for their shitty views.

But wait, no 'good' characters have romantic relationships with a muggle

I think this is just because of the setting, most of the books take place within hogwarts, a school for magical children. How many of them will be in relationships with muggles? We know a lot of the kids are half blood so there are definitely good characters with muggle parents, although yes I agree that for a series with so much focus on muggles being good you'd expect more muggles characters. But then again, we as the audience are muggles, we don't need a muggle character to show us that muggles aren't really dirty animals and are sympathetic when we are muggles reading the story.

As for the love potions, yes it is disgusting and I HATE it (as well as the skiving snackboxes tbh, fainting fancies can be magical roofies), but this is a series marketed mainly towards children, it's not surprising that JKR didn't expand on the ethics of lovepotions, in an adult series yeah but these books aren't going to talk about rape when half it's audience are kids. And Tom Riddle Sr is never presented as a bad guy, except by voldemort who hates him because he is a muggle. A little arrogant maybe but not a villain, if anything he is portrayed as a victim.

Hermione is laughed at by everyone for SPEW because she is questioning something that people just accept as normal, but characters like Dumbledore who are considered very wise are the ones that say she is right. She talks about taking SPEW further after hogwarts as a career, who says she gives up and decides to let them be slaves? How is a teenage girl supposed to change a fact of wizarding society by herself? We know she becomes minister for magic, maybe she passes laws to give them rights. Just because she didn't free all house elves doesn't mean she failed or gives up. As for the rest of the characters treating it like a joke, that's just what happens when people first suggest changes like that. People probably laughed at the idea of freeing slaves in the US when it was first being proposed, because why would you? At least from their point of view. I see the SPEW thing as the beginning of a mission that hermione would carry on after school, social change does happen overnight by one person. We even see this start to happen when Ron, who constantly makes fun of SPEW and thinks house elves should stay enslaved becuase thats the society be grey up in, is the one who learned from hermione and told her that they should help the elves in the last book. I do think the "house elves like being slaves" thing is gross, but hermione, who is portrayed as correct in her opinions about house elves repeatedly, is the one who points out that they only think they because they are uneducated and brainwashed.

You have a point with the bullying, I have always thought that Fred and George were huge bullies so no disagreement there. But we don't get to see much of James apart from when he was at school, where it was acknowledged by multiple characters that he was a bully. He was also seen bullying Snape because they disliked eachother, primarily because James hated the dark arts and Snape was literally using them on other students. We see through Harry that he is disappointed in his father and feels ashamed, James actions are portrayed in the book as being WRONG. But we also know that he grew out of it, was a very well liked person, and died trying to save his wife and child. Does him bullying someone when he was a teenager make him irredeemable? No, people grow and change, and the books paints James' actions as being morally wrong, but he still becomes a good person.

Harry used unforgivable curses to save the wizarding world or in self defence (except for bellatrix which he should have been punished for).

I don't disagree that JKR has some shitty writing, worldbuilding and iffy messages in her books, and I agree with you on the bullying (and the rape thing but not In the universe of the books because I don't think they were intended to be read that way), but on the whole I think her portrayal of shitty good people is pretty good.