It's more likely that the queerrats lobotomized Maria, blamed it on the humans, which caused Mamoru to snap, as opposed to some other grotesque means.
To utilize a fiend, Yakomaru would have to ensure that its rage was directed at the human society, so it wasn't randomly slaughtering them. Substantial brainwashing combined with a very clever ruse to keep the Fiend focused on killing only the human society and its allies. That's only if Maria isn't dead. They also could have killed her in the woods with with poison or whatever, and again, blamed it on the humans. This would also have had to happen recently.
Narrator Saki's words long ago were interestingly phrased. She said that if only Maria had died early on, many many lives would be saved, not that Saki herself had to kill her (referring to when Maria and Mamoru escaped). If Mamoru is the fiend, this makes more sense. He never would have fallen desperately in love with her to the point the he would go ballistic trying to avenge her.
At this point, the queerrats aren't really controlling Mamoru anymore. It's like biological or fire warfare. Release it, and stay upwind.
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As for anyone here claiming to support a particular side, it should be pretty clear that there isn't a "good" side in this entire series. There are no heroes, no one to admire, only villains and our hopelessly lost protagonists, paralyzed by indecisiveness.
Yakomaru is a sociopath who will stop at nothing to secure his ambitions and retaliate against whatever might humiliate him even if it takes years (his queen, Kiroumaru, humans in general). He is exceptionally manipulative. It should be absolutely certain that his "democracy" is a joke. There is no question who truly rules their society. It may have a sort of Senate, but it would be child's play for someone of his skill at manipulation to sway all of them his way over and over and over again. He rarely will even field his own forces unless he is certain of his own safety (often tricking Saki and Satoru into shielding him). He sends the latest subordinate group that his kingdom has subjugated to do the dirty work.
The humans on the other hand, have become as foolish as the Cantus Emperors, thinking that nothing could ever threaten them. Their society as a whole began to treat everything different from them as less than human. They slaughter their own. Their crimes against their own are far worse than anything they have done to queerrats or anything else. Out of fear of creating new Cantus Emperors, they as a whole became what they were so afraid of. It was interesting that Satoru got so angry about what the queerrats had done to their queen, while Saki at least understood that it's not any different from what human do to their own children, equally out of fear.
Yakomaru displays ambition at all costs with no risk to oneself like the worst dynastic Chinese bureaucrat, humans possess an immense hubris, while at the same time constantly cowering in fear about the threats from within.