One Because their existence is mandated by the existence of Mages, with out the later the former doesn't exist.
They are a temporary measure turned permanent.
Two as long as you control the Lyrium, you maintain the control for their behavior, They can become whatever you wish them to be, I do so adore how the Chantry made behavior modification so easy for their soldiers.
And three; We most knew quite a few different people then, most of the specimens of humanity i have met haven't be overly impressive in either regard of mortality or constraint.
So if their own failings and idiocy therefore harm the species, they must be curtailed if they cannot be culled, Magic is a curse to linger at least for now and therefore it must be contained as best as can be.
I get a bitter taste in my mouth when I see people suggest "culling" as a viable option against humans, no matter what their "extra" is.
Even in fantasy settings.
It reminds me that there are people in real life that would like to do the same to other groups of people for various outlandish reasons.
It doesn't help that my grandmother was an auschwitz survivor.
Your "solution" which I assume is to continue as if nothing ever happend, inevitably leads to more suffering and bloodshed.
The plus in a compromise, is that while no one is completely happy with it, it brings a chance for peace.
Violence and abuse usually begets more violence and abuse.
Sometimes you simply can't help it. But if violence and abuse are your first choice, than you are in trouble.
The only thing you need for a peaceful end to the conflict and a better solution, is the will from both sides to make some compromises.