Yes, that is my guess too. Although villain might not be the right term.
Smokey is the Island's security system. By definition, it doesn't like people on the Island (e.g. it killed Parkman when he was trying to use the radio, killed Rousseau's team, attacked Keamy's crew), and if it must allow people, then it scans them to know their intentions (the Others may stay because they really are good people, Eko was killed for refusing to repent).
Jacob brings people to the Island (I suppose to prove that people ultimately have a choice to be good, rather than being predetermined to corrupt as Smokey believes), but other than that he doesn't have any bad intentions to the Island. Hence Smokey can't kill him.
So what was the solution? By appearing to young Ben as his mother, it made Richard believe Ben was special, that he was the Others' destined leader (which he wasn't, hence Jacob gave him a tumor). Then it appeared as Christian, making Ben turn the wheel, and thereby making Locke go back in time. In 1954 Locke told Richard he would eventually become their leader. Thus a self-fulfilling prophecy was created. Locke too was never meant to be the leader. But now that Richard believed so, all that was left to do for Smokey was to send Locke off the Island, where it knew Ben would kill him. This allowed Smokey to take Locke's form and demand of Richard to take him to Jacob. And there, it finally succeeded in having Ben choose to kill Jacob (after first appearing to Ben as Alex and ordering him to follow Locke). Et voil