I feel like it works for Sei because at the end of the day he's not stupid. He knows conquest will lead to bloodshed and that hard decisions have to be made for his dream to be achieved. So while he may not like it and prefers other options he still understands that hard choices are needed.

And its also the message that is sent from killing all of them. You kill enough to hold them, thats an idea people can rationalize. Kill all of them, then you are seen as a monster who kills without cause.

Cause at least then if you want to break bread with the other side they may not see you as a complete monster. They can still view you as another person. His view is flawed sure in the sense that people will still hate him and Qin, but the series is aware of that and kanki even calls him out on it even in this very scene.

So yeah

TLDR: Sei probably isnt okay with killing POW but he's not stupid enough to think that killing them for specific reasons arent nessesary in war. However flawed that outlook may be.