So I stopped reading this for a long time out of frustration, but didn't she have snake children? What happened to them? And what are those spots under her eyes? I'm unwilling to go through all the frustration again lol.
It's not specifically freckles that are found unattractive, it's just facial blemishes in general. But I think the translation and the way the author portrayed it may have caused a bit of confusion amongst the readers. It's like that though because this manhua is of asian origin and in many such regions the beauty standard for women is basically to have pale, clear skin, and to be super skinny with a body similar in shape to that of a child.
So basically to stay alive all you need is a handsome face or else you would've ended up like the group of men harrassing the girl? They portray her like a monster but she'll easily be "weakened" or taken over by loving actions...