The game is rigged for a party play in mind, so you can't kill literally EVERYONE without some consequences that will bite you in the ass later. Also the artifact/the Prism/ the Emperor is also a rigged script in the game that makes you either drag Shadowheart along or drag the artifact along with all the consequences of it being a burden during the interactions with followers of the Absolute. Of course high skill checks can save you from being discovered, but most likely, you will be found out at some point anyway. I am going to continue this after I raid the Grove and continue the story later.