So, I've played through the prologue, chapter 1 and the first part of chapter 2. Now I'm on part 2 of chapter 2 on Ikalis' route (lucky for me, he was the first choice on whose route to go down because he is the bestest boy), and I am really enjoying the VN so far!
I've come up with two competing theories about Ehlly's purple eye colour. My first theory is that his eye colour means that there is a fourth crim and possibly a fourth goddess, the knowledge of which might not be widely known on purpose or has been largely forgotten. I think this is because Ikalis mentioned that Ehlly's purple fur markings have magic in them, and also because of the existence of the Amethyst Heart and the book, which Ehlly's mom, Hilda, told him to hide.
My second theory is that his eye colour means that he has proficiency over both the body and the mind crim at the same time. I reason that a person with proficiency in the mind crim, like Ikalis, has blue eyes. A person whose proficiency is over the body crim, such as Rodrick, has red eyes. If someone were proficient in both, I think it's reasonable to expect them to have purple eyes, since blue and red combined result in purple.
But that's just some theories. Some game theories! Thanks for reading!