Sensei has given the Engineers and Malkuth multiple opportunities to surrender. Beyond the offers to integrate into Human Society, Sensei has offered to cease hostilities multiple times. On multiple occasions, the Engineers shut down negotiations every time, thinking they have the upper hand.
Aris wishes to be friends with Malkuth and the Engineers. Eimi and Toki both wish we didn't need to continue this senseless war. Rio is only doing this because she knows the severity of what Decagrammaton has planned for the world. Himari is only doing this out of her selfish interest in supernatural phenomena. The rest of the GDD is just here on a field trip to support Aris.
Most importantly, Sensei isn't here because he wants to wage war. Sensei came to bring a voice of reason to Decagrammaton. To offer an olive branch to a new form of life that seems to be hellbent on remaking the world in its image. Sensei doesn't fight the Prophets out of some selfish need to prove himself. He's trying to stop an ecological disaster that could end the world. No matter what grand vision Decagrammaton has planned for a perfect utopia, it would come at the cost of the every day lives of our students.
Sensei and his Millennium forces are not the "bad guys" for making ignorant, petulant, misguided children cry over spilled milk.
Every form of life has the right to duke it out and stake its claim for the continued survival of its species. Maybe Decagrammaton should have considered this before indirectly declaring war on all biological life on the planet.