1. It's doubtful that MiB taking the shape of Locke was in their minds at this time.
2. There are many examples of Locke being strangely creepy in S1, and I remember picking up on them, thinking "I'm not sure I like Locke, but I need to keep an eye on him", similar to when Jack turns to Kate at the end of S1 and says "We're going to have a Locke problem."
It's simply a character development. You know there's something not quite right about him, he's got a connection to the island, but at this stage in the game, you're very doubtful of this.
I AM LOST