Christian to me backs up the idea that the island is playing referee, making sure all the players follow the rules. Therefore, he helps both sides as needed. I think the hiccup in that plan was Jacob getting killed.
The island has an interest in people staying/returning to the island, but not necessarily who wins except now the island itself may be in danger, hence the Smokey "Don't tell me what I can't do" rant to the little boy.
There was something involving Charlotte and Faraday in season 4 that invlved some kind of reactor going haywire. Has this ever come up again? It may play a role.