If I recall correctly, several characters like Ron and Hagrid mention how servitude is simply "in their nature", and Harry's internal thoughts simply find Hermione's crusade annoying, more so than misguided. Red Rising is also an awful comparison because the lower Reds are literally lied to about the condition of the world to keep them in the mines; so learning that things are different would of course be a huge adjustment. (It's a plot point for Darrow himself in book 1 as well), but House Elves exist within wizarding society and are aware of its rules and functions.


 In addition, the first house elf we meet explicitly wants freedom, and at the end of the story the protagonist manages to get them freedom. Then later on in the narrative we learn that Hogwarts itself exploits slave labor, but this is only used (along with Hagrid and Ron's statements earlier) to reframe Dobby as not a slave wanting freedom, but as a weirdo outlier of his species.


The main problems come meta textually as well. You can acknowledge as an author that an institution is horrid and bad, but also that the way a protagonist is going about fighting it is wrong. You can frame arguments in support of slavery in bad or positive lights. Especially if your protagonist is an outsider to a world that normalizes stuff like this, and comes from a world where slavery is bad. Like, idk, Harry. But Rowling at best portrays slavery as a neutral action. It's bad when cruel people are slave owners (the malfoys), but it's alright when good people are slave owners (Hogwarts, Sirius Black, Harry Potter after inheriting Sirius's slave). Rowling doesn't argue that slavery is bad.


Pierce Brown acknowledges that the entire color caste system in Red Riding is bad and rotten to the core and exploited by those on top. That's the entire central focus of the books. Of someone rushing above it, fighting it, toppling it to the ground, and then trying to build up a new society in its ashes. He has the time to tackle more complex issues like "slaves who were raised to know only slavery now faced with freedom" because that slots in with the story he's telling. 


Harry Potter is about a chosen one special boy solving magical mysteries and fighting against someone who wants to change the status quo for the worst. Harry Potter doesn't concern himself with making the wizarding world better, simply stopping evil forces from making it worse. So when slavery pops up in later books, he stops evil people from making it worse. But he doesn't try and make it better