The real reason the Doctor let Ian Chesterton remain on the TARDIS had nothing to do with Susan or Barbara. The real reason was that the Doctor and Ian had become friends. And not just any kind of friends, either, but friends with benefits.
Their relationship, they agreed, had nothing to do with Barbara or Susan. In fact, Barbara and Susan didn't even know about it. It was simply that whenever one friend needed comfort, he turned to the other. It was very convenient, and one reason the Doctor didn't try too hard to return 'Chatterton' to his own time.