There are several reasons why it is impossible, or at least very unlikely, that Christian Shapherd was being impersonated by the Man in Black.
1. Christian appeared off-island. It was MIB's stated goal to leave the Island, so clearly Christian could not have been him.
2. Christian appeared to Locke while the left-behinders were time-flashing. Christian appeared to Locke after Locke flashed to a time before the Orchid well was built. (I still don't understand how the FDW could have existed before the well. If you have any ideas, please comment).That means he flashed to a time before MIB was born. Therefore, Christian could not have been him.
Here are some more speculative reasons:
3. When Jack is talking to MIB about his impersonation powers in "The Last Recruit", he says that he chased his father through the jungle on the _third_ day. MIB says that that was him. But Jack chased his father through the jungle, and found water, on the _sixth_ day ("White Rabbit"). Jack was testing to see if MIB was trustworthy. MIB was lying: he wouldn't have known the actual day Christian Shephard appeared.
4. Oceanic Airlines lost Christian Shephard's body in the flash-sideways. Perhaps this is hinting that in the original timeline, they also lost his body. When Jack opened his father's coffin, there was no body inside. The MIB doesn't need to consume the actual dead body to impersonate that individual (see John Locke, Alex, Yemi). This lends evidence to the theory that perhaps Christian was bodily resurrected.
Tell me what you think.