With it coming from a small-business employer who already is obviously prone to shady and deceptive things, I'd assume it comes down to a constructive dismissal via intentionally lowering work satisfaction per your first guess.

...which makes me hope she found this Q&A online and works somewhere like CA that imposes good-faith requirements on at-will employment.

I'm fairly sure letting someone go over refusing to commit what's arguably low-level fraud (blatantly lying about whether fulfillment has already occurred in the course of a commercial transaction) might be treated as a bad-faith termination. In such cases the state can be very employee-friendly, especially if considering it as an official termination then puts the employer on the wrong side of other rules re: other employee protections, final paychecks, etc. The religious aspect would just be icing on the cake.