I will agree that the whole soul thing represents a huge flaw in Dawntrail's narrative. In ARR it is transparently spelled out that we harvest souls and store them in our weapon for our own benefit; these are quotes from the ARR relic quests:

Now, as you may have already gathered, atma is essentially the crystallized soul of a living being. And these crystals hold the key to strengthening your weapon.
Thavnairian tradition holds that the Zodiac Braves gathered light to their weapons by vanquishing formidable foes. 'Tis my theory that the heroes were in fact absorbing souls. And now, through the use of atma, your weapon has been transformed into something with the selfsame ability, and it exists as a vessel for souls. If your weapon is to realize its potential, you must have it drink deep of the souls of slain foes.
So yeah, thinking that using souls as 1-Ups and power-ups is a violation of nature or whatever is a silly plot thread given our history.