You're minorly mistaken:

As Emet explained in Shadowbringers she doesn't kill things she splits them into shards of themselves, pieces of a whole in this case 13 shards and the source means that each person is 1/14th of themselves at the start and with the ardors we've gained some of those shards but were still not whole.

Emet claims he doesn't see the fraction shards as people which is why he has no moralistic delimas with it. ((We have no actual comments from others but it might be safe to say that most of the ascians we fight are of similar mindsets))

Venat however is also not innocent either, though she may not have killed the people of the shards nor the Ancients she's caused just as many problems

In reality she and Organization XIII are all in ambiguous Moral Grey areas of varying shades depending on person and actions and situations