The morality of Halsey's actions, for me, is easy to determine when you realize that she didn't merely abduct children, but also brain washed them. The processes that were performed on them stripped them of their sexuality and their personalities suppressed. By the time they were of age to make any kind of decision, all they knew was the military and that they should follow their orders.
This lead to my interpretation of Master Chief, which I think is somewhat rare; that Master Chief is a human war machine. What I mean by that is that he is a person who was stripped of his personhood and basically turned into a military tool, able to think for himself in terms of strategy and combat, but otherwise he services the military simply because he can't do anything else. He doesn't risk his life over and over out of good will, he doesn't have any personal feelings of affection for the people he saves, he doesn't even have any particular feelings about the covenant. He just follows orders. This is supported by his utter apathy to the medals and public adoration he receives, as well as his complete lack of reservation or questions that the giant bi-pedal land shark monsters he's been fighting all his life are now suddenly his allies. That's just how he views the world, with complete detachment to all life, and nothing exists but the objectives highlighted on his HUD. If the Elites are now suddenly his friends after being an enemy all these years, who is he to argue? And all the people he saved? He would just as soon turn around and blow their brains out against the pavement if the military snapped their fingers and told him thats what they wanted him to do, and he'd do it with no reservations or guilt. All they have to do is tell him they're the enemy. He is a machine, literally a tool who has been as psychologically stripped of free will as a person can be without falling into total insanity to be used as a weapon against any the military deem as an enemy. And you'd never hear him or any of the spartans complaining about it. At this point, this is the only life they've ever known. They're utterly, unthinkingly loyal, no matter what happens.
Of course, the exception to this is Cortana, who is the one emotional connection he has to anybody. All the same, the process rendered them all mindlessly faithful to the call of duty the UNSC rings whenever they want. You don't do that to a person, even in the midst of war. I don't see Halsey as a monster of any kind, as she feels immense guilt over the fact, and that it is the one thing that saved humanities ass in the greatest war they've ever had is something that should be taken into consideration. But to completely alter a person like that seems fundamentally wrong to me.