This bit was painful to read weekly, but looking back it's a very important part. Shin isn't naive, he knows his ideals are childish. But he knows he's backed up at the highest level by Sei, and that he has the strength to make those ideals a reality.
And while yes, the war crimes are omnipresent, it's also true that Kanki's goons are beyond the pale. He has no business acting like he's just doing the usual, either. Sei will have to deal with him sooner or later, because you can't be a benevolent conqueror with Kanki as one of your tools.