Great question! That's what my wife asked. Did Flocke want the sub destroyed? Seems like a lot to continue the con, and unnecessary.
Another thought, maybe Flocke isn't as invulnerable as he seems. Maybe he can off himself. Part of the con of getting them on the sub was them wanting to leave Flocke behind. But he had no reason not to get on that plane.
Or, quite simply, he knew some of the castaways had no intention of getting on the plane anyway. Rememeber, Sawyer's plan was to get on the sub all along (with Kate, Jack, and Hurley). Killing them on the plane would not have worked, as they would not be on the plane.