I'm glad you finally got to the bottom of Molly's condition. Just like with a human doctor, if you can't trust your vet, the relationship is irreparably broken as far as I'm concerned.

As far as your options go, my initial reaction is that I'm a huge fan of raising a ruckus. Of course, I AM a confrontational type. But I probably wouldn't actually go in guns a blazin'. I'd probably wait until they contacted me for whatever upcoming appointment or a reminder or whatever and then advise them, politely, professionally and strongly . You could also file a complaint to whatever state licensing board/association exists for veterinarians where you live.