Rereading IDW. I see now that they took Ian out of Archie but they never took Archie out of Ian. The characters still act as if they're a team who's job is to protect the world. Even after they stop the major threat, they start dedicating their loves to stopping the next threat and cleaning up. This is just something they never do in the games.
I think this is a silly thing to get mad about, so it doesn't bug me. It's a pretty normal assumption to make when the characters spend 90% of their screentime saving the day. It's interesting that this interpretation carried over from archie.