Ben summoned the monster the same way a person might raise a demon, or invoke a curse, or make a deal with the devil, even though they are fully aware that it is the devil. He knows what he did is very wrong or unnatural, but it was the act of a desperate, greif-stricken man who didn't care any more.
The smoke monster is the man in black at the end of season 5. The man in black expresses his dislike for having people on the island. Very well possible the smoke monster helps Ben when he calls his help since the smoke monster doesn't want people on the island in the first place.