WCKD was actually good it was a necessity not a cruelty it was the only high chance way and time was running out it was an absolute necessity. Their other good deed is protecting 107,000 innocent people into a functioning 2.5km diameter city and gave them a normal life, a piece of how life used to looked like they managed to build that in the middle of nowhere in an infected and scorched world. The people lived a relatively normal life their kids go to school, they go to work, they go home, and meet their families and who gave this? the exact organization that torture kids. WCKD also didn't let the outside rebels and people in because, if WCKD opened the city gate and let the people outside in, the city would be doomed in weeks, because not only that the space and resources inside the city was finite, undetected flare virus could spread inside and dooming the ciy.
It was a necessity and it was never out of malice. Even though WCKD's method was incredibly horrific (first of all, it was a necessity) there's a stance horrific means to a heroic good their goal was UNDENIABLY GOOD it ain't power or hunger it's replication and distribution of the cure to the mass to save humanity from extinction.
Thomas is selfish in his own way. By refusing to cooperate with WCKD for a cure, he and his friends essentially doomed the remaining uninfected population to a slow agonizing death. They didn't care about anyone but themselves. They didn't care if not cooperating with WCKD meant millions of deaths, as long as they can live a comfortable life in a beautiful beach.
Isolating the immunes to restart civilization on ONE TINY ISLAND was definitely a dumb. move not only the millions to billions of non immune people left still suffering in the world will now will 100% die without the cure of that enzyme from the immunes and thousands of years of technology, progress, culture, and history are lost forever, now new gen kids from those immunes doesn't have immunity, and them getting flu or some minor Diseases will be deadly and could become extinct fully, ESPECIALLY BECAUSE THEY RESTARTED FROM STONE AGE AND ONLY IN ONE TINY ISLAND, ALL THE NEW GEN "REBUILDER OF CIVILIZATION" ON ONE TINY ISLAND IS VERY VULNERABLE TO EXTINCTION THROUGH MINOR DISEASES
WCKD didn't fail because their logic and science was wrong, they were right! Under extreme stress, those immunes produced a unique chemical for the cure, they only failed because Thomas and right arm kept sabotaging them, if they didn't do that, they just need to catch Thomas, and the world is restored! Moreover Thomas should've cooperated from the start and another moreover he knew he was the cure before WCKD he knew it in the end of scorch trials seeing how Brenda healed from the enzyme in his blood he should've surrendered from there.
while WCKD killed many immune tennagers without results, how could they have known which kid had the right enzyme for a cure? that's the problem, their science was right,just they didn't know which kid had the best enzyme, and they could have never know that, i mean sure they were always hoping that one specific immune's enzyme was strong enough for a cure but their intention was good and they chose the method with the highest probability of expected success outcome
they were justified under Expected Utilitarianism the enzyme wasn't strong enough was a bad moral luck that they can't predict who was the cure and who was just slowing it down.