The scene with Sam and Karli is not Sam feeling real sympathy for Karli. He's empathizing in an attempt to talk her down and get through to her, to try and get her to turn herself in or at least change course. It's pretty standard de-escalation stuff. You'll see cops do the same thing in hostage negotiations, for the same reasons. It doesn't mean they're suddenly in agreement with the person they're trying to de-escalate.
And we know Sam has strong training in this kind of thing; they made that clear.