DISCLAIMER: This is going to be more of a way to help you understand how other places have a blue and orange morality and how the main character's goals still make some sense using a children's movie. I won't be able to link everything from your story to the example, but I'll try my best to explain.
WARNING: Spoilers for The Nightmare Before Christmas
Think of it with The Nightmare Before Christmas.
Just in case you have never watched the classic movie, The Nightmare Before Christmas takes place in Halloween Town, where Jack, also known as the "Pumpkin King", scares children every Halloween. However, he grows "tired" of scaring children "every year". Sometimes they even physically harm humans or animals:
Robin Thomas (Mayor): ... most of the blood drained in a single evening.
This was rewarded to the vampires, so as you can see, their morals are certainly more alien than ours, which is the point of the Blue and Orange Morality concept.
So why do we root for the main character, Jack, if he's scaring children, or understanding his morals?
One of the reasons that Jack is such a great example of a well-created Blue and Orange morality character is because his motivations are reminiscent, but not complete, with our (human) motivations.
For example, Jack tells his dog Zero that he is tired of scaring children. This is the core of his motivation for the whole movie. I'm going to write this down to resort back to for this section:
Jack the Pumpkin King has grown tired of scaring children year after year, and wants to do something new.
No, he did not have a change of heart and decide that it's morally wrong to continue to torment innocent mortals. Instead, he just got tired of doing it. It became repetitive, a chore that he has to do every year. Notice how the concept itself, on a literal meaning, is really insulting to the children themselves. He gets bored of doing something that could leave a child traumatized for life. But, really, if you think about it a little more, the situation he's in is more relatable.
The situation for the reader who is (probably) human isn't getting tired of scaring little kids. Maybe it's just being tired of school or work. Maybe it's feeling like your schedule is the same one over and over again. Even though a human wouldn't like the torturing aspect of it, they can relate to feeling like they're forced into one thing forever.
Moreover, Jack is looked up to by the Townspeople because he's by far the most frightening. Obviously, not many humans look up to being frightening, but maybe they can relate to the concept of the feeling. For example, a child may feel like they relate to Jack because their family looks up to them to be the next best doctor when really they feel like doing grades is a chore. Both characters feel backed up into a corner. It's just they both have different morals or "extremes".
Overall, when trying to pull off motivations with an Orange and Blue morality, don't think literally, think more abstract. Find the theme of their motivations.
The surface-level motivations for Jack would be that he has grown tired of scaring children year after year, and wants to do something new.
The surface-level motivations for the student are that she has grown tired of working on her grades for her parents, and wants to try new things.
However, at their core, they both share the want to do something they've never done before, instead of feeling trapped to do one thing forever.
Let's go back to The Nightmare Before Christmas. When Jack finds Christmas Town, he reacts to everything like he had been transported to a brand new world. He has never seen festivity before, so of course, he explains how interested he is in it. What this results in, is him trying to understand how to use something so foreign, and jumping to conclusions as to how to do it. In fact, I'll go through the two that really explain his judgment, and how well the writers did what they did.
1. He thinks he can just steal Christmas
Once Jack realizes that Christmas spreads positivity to children every year by giving them presents, he thinks he can do it himself with the help of Halloween Town. Now, this may sound stupid on his end, but the audience can actually see why he would do this. It's paired with his judgment and motivations. We already know that Jack wants to try new things, so motivation is down. However, his judgment is clouded.
Jack has been known as the 'leader' of Halloween Town for years. He had no prior knowledge of the doors and therefore doesn't understand how each place has its own ruler. He has just learned about Christmas. Jack has been put on a pedestal for years and never really told to stop, so he thinks that it'll be the same for Christmas. He thinks that, like those in Halloween, that he can direct what goes on in Christmas Town. He vaguely knows there is a man in charge (Santa Claus), but he thinks he'll treat him just like his Mayor, who also puts Jack on a pedestal and listens to whatever he (Jack) tells him.
This isn't surprising, though. While it's hardly to this degree, this is one of the causes of narcissistic, "bratty", or whiny behavior: having no real respect for authority because you were never taught to.
Therefore, we can see why his judgment is this way here.
2. He Tells Three Children to Kidnap Santa Claus
This goes with #1, but I felt like this really reflects more of the Orange and Blue Morality in this particular action. You can really see his judgment is clouded when he tells Lock, Shock, and Barrel to get Santa Claus and tell him he's going on a vacation this year. We know that Jack is in the wrong, of course. This is Santa Claus' holiday. But when you think about it, it makes sense! He lives in a world of Halloween, where the torment, stealing, and killing are real. This is what he thinks is right. It's no different than a child screaming at their mother to let them use the shopping cart in a store. Just to a degree that most humans wouldn't agree with.
So, what about judgment? It can be (humanly) morally irrational, but make sure it's supported by motivations, character upbringing, etc so that your character isn't viewed as plain evil.
Hopefully, this helped answer some of your questions!