Sacrifice the hand to save the body. Machines have an inherent advantage, and in order to human to minimize the gap and have a chance of surviving, it is necessary for them to mimic machine efficiency as closely as possible. That means being absolutely cold, rational and ruthless. In theory, as long as enough of the population was present to ensure genetic intergrity in future generations, the rest are dead weight.
That's what bugs me about both the Matrix and BSG. The machines are vastly, vastly less powerfull mentality than they ought to be, because it is literally impossible for a human to outhink a machine of human-or-above intelligence. Even taking into account human unpredictability, a machine should be able to plan for every contingency far better than a human could.
And besides, Cain adds spice to the show. It's no fun now that Adama and Roslin are all buddy-buddy and the crew can pretty much do as they like. There's no conflict. What would be really interesting is if Cain actually succeeded in taking command of Galactica and ran things while Adama & Co went underground and staged some sort of coup. That, or Roslin getting a new body from the Cylon ship.