I have finally realised why MiB couldn't kill Jacob. Notice the similaraties between the poison-type Pokemon Weezing/Koffing, and The Smoke Monster. I know, I know, you're all facepalming right this second. "Why didn't I realise this sooner" But it is true.
Quite clearly, The Smoke Monster, which we now know to be Koffing, is not effective against Jacob. Koffing is a poison type pokemon, and what is the only pokemon-type which poison pokemon have no effect upon? This Chart clearly shows us that if a poison pokemon were to attack a steel type pokemon, it would have no effect. So - Jacob is clearly a steel type pokemon. This would obviously explain all the electro-magnetic doo-whacky crazy type stuff we've seen on the island. A powerful steel entity like Jacob was sending the island a bit mental with electromagnetism (somehow) and MiB was fed up of it. MiB's weakness to steel types sought him to rid the island of steel type pokemon once and for all.
But Smokey was clever. He realised he needed a pokemon that was super effective against steel-type pokemon in order to eliminate Jacob. This handy chart once again shows us that either a fire, fighting, or a ground pokemon will do when attacking steel type. So up steps Ben. Clearly, whatever type Ben is, he is super-effective against Jacob. Ben used the move "stab" - twice for good measure. For added security, MiB kicked Jacob into the fire, one of Jacobs ultimate weaknesses.
Notice the blatant similarity between the two entities