Hasn't it already been confirmed in an interview that Mara wouldn't appear in the game? So far as I know, all the MP skins are from the SP game, so Mara most likely won't be there.
She has no reason to be there, anyway. She probably has very little to do with Kyle at this point. As for Jan, consider that she is still a Rebel Agent during MoTS, so you should figure that she was off on a mission during the events of the game.
Mara is a really cool character, and there are some excellent artists in the MOD communities, so I'm sure it's only a matter of time until we have whole MODs focused on her, plus some great skins.