If you choose to remain and work under her, which it sounds like you're inclined to do, I would journal/document any interaction with her that might be construed as tense, controversial or "disloyal" [from her point of view, not necessarily yours]. Don't tell your coworkers you're doing it b/c it will just look like you're a troublemaker. In the event there's ever a "she said/she said" situation, her superiors will be inclined to side with her based on her position. Your documented facts will offset her advantage and may protect you.
I hate to sound cynical, but the type of person you are describing will lie to protect themselves...
I’ve never known her to lie but she does seem to have an agenda.
This is excellent advice, especially when you know you are in a tense situation. Don't let yourself get blindsided and feel helpless after you are laid off five minutes before some important deadline that will affect your retirement.