Ben lets Locke blow the submarine up so Jack and Juliet are stuck on the island, and he doesn't even get his hands dirty.
The sub is an illusion; Ben says it is only there because some people arent's ready to make a full "commitment" yet, and it maintains the iillusion of freedom to come and go as they please.
This is exactly my point it maintains the "illusion" of freedom and you're right that did come straight from Ben himself. I don't think the sub works.