I'm not sure Anna is Freplica, but I'd be surprised if we didn't see her come back before the show is over...she was so active in the first few episodes. I don't think they'll kill off Freplica this season...although it's (in my mind) highly likely that she'll be discovered and will become one of Sark/Sloane's agents of evil...wahahahahaha. As for who dies...my vote is for Emily, if anyone. But like it says, people who die on this show are never really all dead.
"Ooooohhh! Look who knows so much, eh! It just so happens that your friend here is only mostly dead. There's a big difference between mostly dead and all dead. Please open his mouth. Now, mostly dead is slightly alive. Now, all dead...well, with all dead, there's usually only one thing that you can do."