Bro, do you hear yourself?
She serves in an organization that maintains secrecy, has a clear hierarchy, discipline and goals that are known only to some extent to its agents. In this sense, there is no difference between the Order and any agency with three letters. She is just as brainwashed as the average soldier, police officer, detective or government agent, she serves and protects.
Decisions that change the past are entirely the developer's fault.
On the other hand, they add additional variability to the game and make it more interesting. If you don't like the way Kaija treats you, it's because of your choices towards her, and you alone are to blame.
A skirt is just a skirt. I've seen shorter ones, I've seen more revealing ones. Right in this game. Not associated with any sluttiness, in no way indicating that the owner of the skirt is a whore. These are your prejudices, nothing more.
By the way, if you saw her, MC and other people in their outfits when they were in Neverwhere, then the skirt question is disappears on its own. She was probably in Neverwhere before she came home.