Fired for choosing not to allow employer to deduct my pay?

Subway is a national chain. They have HR offices and people to call with concerns about things like this. I would find out where you need to call for your district or whatever and give them a call. Legally your choices are to pay her back or get terminated, but I have a sneaking suspicion that Subway will not approve of what she's doing. If you want to keep your job in the short term, pay her back the money and also send her a letter explaining that you do not agree with her fine, and send a copy of this letter to the corporate HR office.