Students who treated him like shit and beat him up, vs the civilians of the (probably) largest city in the Kingdom. The attack is targeting everything and not just a single ship. He only has Partner and not Luxion's true body as a trump card since it is out of contact range.You make it sound like it's some awesome character development, but regrettably I'm seeing little of the anguished decisions you describe in the story.
Instead, all I can see is an MC that, so far, has gone to ridiculous lengths not to kill anyone, suddenly saying that "mercy is out of the question". But apparently, when it was an army against a single boat filled with students, mercy was still an option. Go figure. This has plot convenience written all over it, and I honestly expected better from this series. Making the MC drop his "no-kill" policy should be a huge thing, not a footnote that goes against his established characterization.
The situation is vastly different in terms of scale and forces deployed.