In The Thousand-Year Blood War arc, Mayuri killed 28,000 Rukongai citizens in order to balance the soul count. According to him, this was done because there were a lot of Hollows disappearing, causing an overflow of souls in the Human World. If Mayuri 'killed' souls in Soul Society, wouldn't they reincarnate in the Human World, causing even more soul overflow?
The way the balance works is thus:
- A human soul existing in the Human World does so either through the birth or death of a human.
- This soul can either be purified and transferred to Soul Society by a Soul Reaper, or transform into a Hollow either through worldly attachments or possessions, or if a Soul Reaper doesn't get to them quickly enough.
- Soul Reapers can purify the transformed Hollows which allows their soul to re-enter the cycle.
- Souls that exist on the other side in Soul Society can eventually re-enter the cycle.
Ultimately, the objective is to maintain net-zero - there are enough souls that are either Plus, in Soul Society, or are Hollow - but none should be taken from the cycle.
The way that a Quincy destroys a Hollow would prevent their soul from ever re-entering the cycle, thus the balance becomes lopsided. If the Quincies destroyed 28,000 Hollow, then there would be a surplus of 28,000 souls in Soul Society. Thus, to maintain the balance, those 28,000 souls would have* to be destroyed; they can't reincarnate since that would preserve the imbalance.
*: Although this does raise the question, why not allow half to reincarnate immediately, but...Mayuri's methods are pretty blunt and direct. The thought may have never occurred to him. Plus, there's no directly stated method that a Soul Reaper can cause a soul to immediately reappear in the Human World.