I'm compelled to point out that Wes has been adamant about internal threats in the Empire being diminished, and that SAINT be painted as more trustworthy. As a Yamataian plot GM, I'm compelled to push in this direction. Kotori has her bias against SAINT, but she also has evidence to back SAINT not being as troublesome as was feared as well.
In this plot (and those preceeding it) Doshii and I have been drawing a lot from how SAINT spooks would eliminate anything that became 'inconveniently knowledgeable'... but this hasn't been something that Wes has pushed in a loooong time. This feels a little meta, but I'm making an effort to steer things more into a direction he'd prefer.
Kotori, in turn, is being objective (despite her dislike and suspicions) because she actually has little tangible fuel to feed the fire. People suspecting this has something to do with her lover being a SAINT agent is also a viable avenue to consider.