I don't think they're manipulating Locke into a leadership role. Richard went and visited Locke as a child before Ben was even born, which hints at him always having an interest in having Locke on the island. I do think, though, that Ben himself was trying to manipulate Locke's natural ascension to leader to his own advantage.
I think the exchange between Richard and Ben was more a reflection of Richard momentarily confiding in his past leader than a peek into some ulterior plan they have going on concerning Locke. It could also point to maybe they both knowing something about Jacob that they don't want known. That could be their shared conspiracy, I suppose.
Let's not forget that when Richard tested Locke as a child, he failed the test.
Others may have a sharper memory of events in Locke's life than me, but I can't think of an independent source that in any way confirmed Locke's leadership qualities. Mostly, the source of this is Ben. He told John he was to be the new leader, later confirmed by Richard. It was Ben who told him his father must die first and that he would have to die to bring everyone back to the Island.
Suppose Jacob does not exist. That he was totally a fiction of Ben and other leaders used to keep the group in line. Suppose further that when John "sees" Jacob, that tells Ben that he is the most susceptible person to Ben's constant suggestions of his leadership qualities. As we all know, until this return to the Island, John was never a leader. He learned his leadership skills during his time on Island as he grew into his new Ben-given identity.
I still think that the short conversation between Ben and Richard could not have occurred if they had absolutely no control over John's assent to leadership. Saying that he is going to be trouble for them implies that they had other choices and that somehow they still have control over the bigger picture and may be using John as the figurehead who will be available to be sacrificed in whatever conflict lies ahead.
