I'm thinking maybe someone will just have had a soft spot for her, though gosh knows she didn't deserve it. And smuggled her out of danger. Mostly.
She did make a deal to help them assassinate someone, and was supposed to get safe haven as a result...but what bothers me is that they continue with that deal after the amnesia. If she doesn't remember the deal, why do the bad guys bother with honoring it? On the other hand, after the amnesia she's not much of a danger to them, either...she doesn't remember any details of their plans. And because of the way she lost her memory (this is sci-fi stuff), she's not going to just remember it again later, so she's out of the picture.
Even so...why not kill her to be sure?