I think that Ben's actions must be judged on the basis of just how special the Island is. (Thats very special, mates) Exceptional circumstances call for exceptional decisions. We don't yet know enough to say, but I side with the fact that Ben is doing what he feels he has to.
He isn't evil, and he doesn't enjoy causing people harm. He is too classy for useless destruction.
There are worse things on the horizon for the Island that, right now, only he understands. Oh, sure, Jack thinks he knows where it's at, but he don't know "jacked"!! ;)
I say, trust Benjamin's judgement, because he always has a plan. Even if he shoots people and treats Juliet the way he does along the way...