It's only a matter of scale.
Kidnapping children and covertly murdering people, bringing extralegal justice to save humanity was justifiable to younger Halsey.
Killing a few people to save the galaxy is justifiable to Cortana.
The Gravemind called it years ago—Cortana's big weakness is her desire for knowledge, and the only thing that kept her from pursuing drastic measures was her actual ability to effect them. Come Halo 5, those limits are removed, and she's coming off having been treated like crap by the organization she was built to serve (and whose goals of control likewise match hers) save Master Chief.
It's not just a matter of scale.
Halsey decided that she needed child soldiers in order to quickly end the war. She kidnapped them because, obviously no one would consent to this. And some died because it was a dangerous operation. This is terrible, Halsey's a piece of shit, we all agree.
Cortana decided that she needed Guardians to quickly stamp out aggression between warring species. OK She extracted these Guardians via surprise attacks without evacuating population centers because.... She's like Halsey? Why did she execute in this way? It doesn't make any sense.