The first time Smokey and Eko confronted it was probably exactly what happened when Locke met Smokey in Walkabout. Smokey scanned Eko and read his memories. It saw him as someone valuable to its motive of killing Jacob, getting a body and leaving the Island.
But later when it met Eko, Eko admitted he was damaged by his past. He did not regret what he had ever done. He was not easily manipulated. Smokey didn't like that, so it got rid of him. Eko had become a threat to his plan.
Locke remained weak, and was easy to play. So it continued its plan using him.