Reprogramming a Robot doesn't mean killing it – it means improving and adjusting. In such a case, improving, adjusting, and, I guess we can say, reprogramming, are necessary. It's just like chemical castration. Habitual rapists who undergo chemical castration could be reduced their libido and sexual activities effectively. But they are still able to have children; they are not actually castrated, nor are they sterile. It's good for everyone, isn't it?
As for that Sentinel, from AA #32 and #33, we could see clearly it still yelled out "Kill all mutants" even in front of X-23, and attacked Emma directly when she just arrived at the Avengers Academy without doing anything. Juston's Sentinel is an X-factor that is highly possible to hurt any mutants.
We all know what Sentinels are, right? The giant robot killing machines designed to genocide the mutantkind, who should be responsible for unending massacres of mutants. For X-Men, especially Emma Frost, whose most students was killed under the sentinels' barrels, the very existence of one of the killing machines right in the school of their (former) ally is not only a threat but a kind of insult as well. And even in such a case, Emma gave up smashing the Sentinel, just want to remodel it and remove its mutant-hunting program creating a new persona for it… Even Dr. Pym and Quicksilver both agreed with Emma's suggestion, right?