Unfortunately, the database entry for Connors mother pretty much spills the beans beforehand if you decide to read it, so it pretty much just confirmed it for me. It was still a really clever and well executed twist, but they really shouldn't have put that in the database entry until after the fact.
The thing In Kaniehtí:io database I didn't really get I was thinking wait why is she helping the temps too? I had a feeling something was fishy about that whole start thing and as soon as Haytham was inviting Charles Lee into the Order I was like "Why isn't he saying the Creeds rules and stuff?" and as soon as he said "May the Father of Understanding Guide You" I was like "OH F****ING GOD!!!!! WHAT THE F***!!!!!!!"