Yeah – the credits list her as the mistress, so I tend to go with Thomas’ mother either having been safely back at home or dead when Flint killed Alfred. Not that that makes it any better, but at least Thomas might have had one parent that wasn’t completely awful.
I always felt like Thomas’ mother was likely dead because you never heard mention of her. Not from Miranda or Thomas or anyone. When Abigail talks about the story her father told of Captain Flint killing Alfred Hamilton, there is still no mention of her. If the woman with Alfred had been his wife you’d think it would have been mentioned that Flint killed Alfred and his wife. That would’ve added to the “monster” England was branding him. Perhaps she could have been Thomas step-mother, happy to see him “disappeared” in hopes of having her own child with Alfred to inherit everything.