Well, my first question before getting to the end of your post was have you tried giving meds? If it is teething pain, those should help some. And, if you give them at BT, they should last through the DF and would be given on a full tummy so shouldn't cause too much upset.
Is her daytime routine still going well? I guess if you're worried it might be becoming a habit, I'd do what you can to get her back into her crib. Can you hold her for a bit after the DF and then transfer?