I look at it this way. Both zodiark and crystal mom are evil. Too much of one and boom no one survives. What I glean from everyone's point of view including the emperor is that if all the shards are rejoined a new world will appear with both bad and good people in balance, some suffer and some don't. That's life. I also like to refute the idea "well killing millions is evil no matter what" and I would like to point out killing them now, gets it's over with and prevents more lives to be lost to the light and dark and the ends justify the means. It's like a trolley cart scenario. Death is inevitable, so I think the best way to go about it is to end it quickly and with certainty.