I guess there are reasons for both options.

For killing
-confirm that Millie really is a stalker 100%. Sure, we are 99% sure but the mayor has blue scales too. Its not impossible that he locked Millie in the room with the evil essence to make her think she did it and frame her, like what happened to Jeff. None of the other stalkers seem to feel guilt or act weird during the day so maybe she only feels it cos she isn't a real stalker! It's a long shot, but it would rule it out 100%. xD
-no real evidence that there is a difference between killing now or by ritual
-more innocent Pokemon will die in meantime

Against killing
-its possible the ritual does something different to souls, but who knows
-neo confirmed that even if there are less stalkers, there won't be less kills, so we won't necessarily be saving Pokemon anyway