For me, it's not an ACTUAL government doing this. It is made up. Make believe. And the same way I can root for Dexter (good one), Walter White, Scorpius, and other protagonists who do otherwise horrific things, I'm fine with this. Star Trek does ALL KINDS of unrealistic things, from tech stuff like transporters and universal translators, to behavioral stuff like lack of money, the joint exploratory/military that is Star Fleet, or an entire planet wearing the same aluminum foil jumpsuits. If the actual CIA was putting Jeffrey Dahmer or Osama Bin Laden in charge, I would care. I do not care at all if it happens in a fictional environment and leads to stories I find entertaining.