What antibiotics is she on for the bacterial infection? I think they often use metronidazole for liver disease.
A vet is never going to criticize another vet's treatment to a client. It just isn't ever going to happen. I would completely stop the Comfortan, but I perfectly understand if you are not comfortable doing that.
I'm so sorry to hear your news, but it is not unexpected. You are a wonderful owner to Megan. Remember that she is not afraid and lives in the present moment. You rescued her and gave her a happy life, and she loves you very much.