I'm always annoyed when people try to apply moral ambiguity to destroying the Death Star and other such moments in Star Wars; it indicates to me that they're entirely missing the point. From the start we're told that it's the "Evil Empire" and the Rebellion is the good guys. Having a clear-cut view of what is good and what is bad - that's what makes Vader's redemption possible. He had to be bad for his redemption to mean anything. That's where the morality becomes sophisticated, not in imagining the Death Star to be full of innocent civilians.

On a more emotional level, I just find it more repugnant to watch the characters in The Matrix plugging everyone full of holes like a video game, compared to the mild violence in Star Wars. Their blank faces are so lifeless. Like they don't contemplate the morality of what they're doing because they are fundamentally utilitarian, as robotic as the machines they're fighting.