Finished the MSQ - Feels bad, pushed to do evil [Spoilers inside]

[Kaecilius]

They are computer programs running the dead's memories over and over again ad infinitum.

This is incorrect. The moment they show sentience and the ability to learn and change they are entirely new lifeforms based off a copy of the previous one. We can say that machines intelligences don't deserve the same moral consideration as flesh and blood beings, but we are also buddies with the Omicrons that might find that a bit problematic.

My WoL would happily shut down the simulation rather than go and start harvesting the souls of the billions of innocent lives in every reflection for the benefit of the tens of thousands in the simulation.

Sure, so did mine. We had to stop things from escalating. But once again, there is no weight given to what we're doing, because the narrative doesn't want us to even consider the possibility of moral nuance. They are wrong and unnatural, and we are right and the good guys.