That's a dilemma, especially if the programmer/reprogrammer clearly benefits from molding the sentience according their own requirements.
But - BUT - what saves is a bit is the way "Visual Guide" describes what Cassian actually did: one of the core directives of Imperial droids is to recognize and listen to order of all the high-ranked officers. Cassian did not simply changed it to "listen to the officers of the Rebellion right now" but REMOVED the part of the programming that dictated listening to authority. That's why K-2SO is able to act pretty unconventionally and decide for himself. That still doesn't remove all the controversies but IMHO makes it much better.
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But - BUT - what saves is a bit is the way "Visual Guide" describes what Cassian actually did: one of the core directives of Imperial droids is to recognize and listen to order of all the high-ranked officers.
Cassian did not simply changed it to "listen to the officers of the Rebellion right now" but REMOVED the part of the programming that dictated listening to authority. That's why K-2SO is able to act pretty unconventionally and decide for himself. That still doesn't remove all the controversies but IMHO makes it much better.