The necessity of queerrat biology in Shin Sekai Yori
(Major spoilers here.)
The following is probably obvious, but once you start following the dots at the end of the show it's clear that what happened with the queerrats is almost inevitable. Right now I feel like laying out why this is so.
A core ingredient in the precarious stability of Cantus humans is death feedback, which makes it so that almost no Cantus human can use Cantus on another human to any dangerous degree. In its flashbacks to history the show gave us a fair number of examples of what happened without this precaution (and then the false minashiro explained it). But death feedback presents a problem for Cantus humans as they interact with regular humans, especially after the history we were shown. Put simply, Cantus is what keeps Cantus humans safe from humans but death feedback means Cantus humans can't actually use it; regular humans are thus free to come after Cantus humans with everything from sharp rocks to firearms and kill them all.
This gave Cantus humans not very many options. They could completely wipe out regular humans, they could somehow completely isolate themselves from regular humans (and make a very big bet on that isolation lasting forever), or they could somehow make it possible to safely use Cantus on regular humans without invoking death feedback. The latter is what they did: they made regular humans non-human enough that they would not trigger death feedback (or at least that they would not usually trigger death feedback; as we saw during the show, killing queerrats can still trigger it under some circumstances). Cantus humans still needed to keep an eye on queerrats, especially initially; as Squealer showed, Cantus is not guaranteed protection in many ways.
(I suppose they could also somehow make it so that regular humans couldn't attack Cantus humans, but I don't think that that's a reliable protection. Note that death feedback itself is not reliable, cf fiends.)
I don't think that the Cantus humans initially warped humans into queerrats to have slaves. I think that was just a side effect of having queerrats around and keeping an eye on them.
I see the biology of queerrat queens as a measure to make it easier to control and limit queerrats. Queerrat queens are implied to be large and mostly immobile, and they are the only breeding source of queerrats. This makes it much easier to keep track of them and much easier to eliminate rogue colonies (just kill the queen and ignore everything else) and control the spread of colonies. Cantus humans were undoubtedly already very familiar with how hard it is to control the population of people who can breed freely and widely.
The morality of the queerrat rebellion in Shin Sekai Yori
It all started when @A_Libellule and I got into a Twitter discussion about this particular issue. In the course of the discussion I had a realization about my core moral position here:
If a group has to choose between living as slaves or committing genocide, picking the latter is morally legitimate.
It would certainly be nice if the queerrats (and interested Cantus humans) could find some solution short of genocide (genocide is ugly and invites counter-genocides and so on), but they are not obliged to do so and they are not obliged to remain slaves instead of committing genocide. The Cantus humans lost all moral standing to complain about it the moment that they started keeping queerrats as slaves (and, lest we forget, wiping out entire queerrat colonies when they felt like it), just as if you try to keep someone as a slave you lose the grounds to complain if they kill you to regain their freedom.
By the way all of this applies if a group is choosing between living as slaves or 'merely' killing some (significant) number of the people keeping them as slaves. I am just taking it all the way to genocide as an extreme case.
(Naturally this deeply colours my view of Squealer's rebellion and his fate and also my overall views on the Cantus humans.)
I could go on at greater length here but I suspect that this is the kind of thing where either you agree immediately or where you are not going to be convinced at all.
Note that you can make a functional argument over whether the queerrats were going to commit genocide or simply kill some number of humans and then stop. My personal view is that they were going to have to go all the way to genocide and they knew it; one surviving breeding pair of Cantus humans was potentially all that was necessary to take over the world again and destroy all queerrats, so none could really be allowed to survive.