I was weirded out by the Illustres' choice as well, but further thinking on it I agree with his decision. Yes, the omnicidal version of qwardians that Kalmin wants are more dangerous, but, they are relatively self contained, in fact they are like Apokolips.
Darkseid and his armies have the ability to wage a devastating war on the rest of the universe practically whenever they want, akin to the Annihilation Wave that happened in Marvel a while ago, and impose his tyranny that way. They don't do it because Darkseid wants the Anti-Life equation and to do it with just "one button", instead of "having to work for it", so they are relatively self-contained.
The qwardians like Kalmin want to destroy the universe and everything in it because they believe and follow the Anti-Monitor, but they are dedicated to creating more and better destructive weapons (Weaponers) and training to be more efficient and better warriors as the army of the Anti-Monitor (Thunderers). They already have qwa matter, if they wanted they could build a fleet with a bunch of qwa energy weapons and qwa matter bombs and fly through the space just blowing everything up; not even the Illustres could escape/survive a qwa matter bomb of enough size. So they are self-contained because they are waiting for the Anti-Monitor or until they find the perfect weapon capable of destroying everything with "one button", instead of "having to work for it".
If the Illustres let Varnathon continue his plans he lets a new Evil Empire be born. Right now, Qward doesn't have an empire, they are just extremely dangerous and sometimes commit some atrocity or another, same thing with Apokolips like Canis Minor said. So, if Apokolips can be left alone until a proper solution is devised for them, the omnicidal qwardians can be left alone as well, instead of letting them become an expansionist, evil empire that would have access to qwa weapons, a pretty good trump card against anything else in their universe (that we know).
TL;DR better to leave Qward in the hands of the omnicidal crazies because they stay in their planet, than let them become an empire that would expand and become a headache in the same level or worse than the Reach.
