She’s just confused, with everything that’s gone on with her memory and everything else.
But she has feelings for both of them, that’s why she asked. But if Rory doesn’t want it, she won’t force it. She doesn’t want to lose either of them.
@SubIimeEnigma
It's so weird knowing her boyfriend is now a girl, but that doesn't mean she loves him any less.
In fact Warren had let her into the Manor and she's making her way to the room that her boyfriend/girlfriend is in and knocking on the door