Yes, but as you (and possibly Stirling - although Alyx may have a lie to feed him) may have guessed, Alyx might not have been entirely honest when she said she didn't know Janathan.
And the whole reason she's in this mess is that she's not actually a very good assassin. Not necessarily as regards her ability to kill people, but her willingness and how her emotional attachments affect it.
Janathan, unless he panics her again, is probably not at any great risk of Alyx killing him.
As regards Remar, it did sound a little bit like the Pistachio Grievers might have already done something regarding him. But if it happens they haven't, Alyx has an idea that could be quite fun.