You can't produce effective elite soldiers by torturing the hell out of unwilling subjects. All modern special ops programs rely on getting the most heavily motivated volunteers they can. No one else will get through the training. The idea of putting unwilling subjects through Training From Hell and getting brilliant results is fiction. You'll mostly get brittle mooks with major mental problems.
This is the same kind of nonsense thinking that makes people think standard torture techniques are effective. There's some part of the brain that wants to inflict pain upon the enemy, and wanting to get information out of someone provides a convenient rationalization for that sadism. If your goal is to extract information, use sleep deprivation and you'll get results. Waterboard someone and you'll get lies or fiction you want to hear. If you still feel like torturing people, you're an ineffective sadist, not a hard man doing what needs to be done.
You need to ask if your real goal is living out sociopathic power fantasies by torturing people, or whether you want to really create elite soldiers. I've always had the impression that Cerberus had far too many people whose only goal was to justify their wannabe badass personas by finding increasingly creative ways to make 'difficult decisions' that secretly appealed to their sadistic and xenophobic natures. I'm sure there were some sensible pro-human types there too, but these borderline sociopaths tend to be power-hungry, and those are always the people who end up in charge. (No special reason, they just try much harder.) After a while, the whole organization is conducting worthless experiments and wasting its assets, because the people in charge don't really want to help humanity.
This isn't a Cerberus-only problem, of course. Such mismatches between an organization's goal and the true goals of its power players happen in any institution that exists long enough. And the worst part is, you generally need the sociopaths, because they're surprisingly good at getting things done if they're properly focused on the real goal. If nothing else, you need a few really smart sociopaths focused on the real goal because they're the only ones who will unhesitatingly neutralize the dumber sociopaths playing their useless games.
Shepard is a surprisingly good example. Renegade!Shep tends to go too far into sadist territory, but somewhere in between Paragade and Renegon is the ruthlessly focused operator who really will do what needs to be done, without falling into the dark crevices of his nature.