So, Claire refers to not being alone as she talks with her father and her "friend". I believe that when people are "infected" they can see MiB for who he really is at all times. So Claire would be able to diferentiate her "friend" and Christian. So this brings up the big Question, Who is Christian and what are his motives. I've stated this before under a different Blog Name (I was listening to Clapton and thought of this one and changed it), But, I believe Christian is the voice of the Island.
This could be why he sometimes is pushing people to do things that serve MiB's benefit or just showing them the path they need to take to fulfill their destiny. Because, you might need to do a little bad to survive and that is what the island is trying to do.
He isn't on either Jacob or MiB's side because he has his own agenda, the island's agenda and that far surpasses the white/black conflict.