Sure. Both sides could use the fallen as their new soldiers. They could retrieve info and reprogramm the synths either freeing them from the MC or bringing them back to hive.
The question is not just why but also how. Cybrex used to be a united machine consciousness. How could one part of it change its ethics and other not? Hive minds are free from factions management, after all.
It is said that Kuurs created a sentient machine which leaded to rebellion not that they opressed sentient synthetics population for a long time. So probably their robotic workers were not conscious. It seems that they just invented the sentient AI created a test sample and then things went wrong. The AI escaped, took controll of the robots and became what is known as Cybrex. But then it developed. The cybrex drones became sentient they started understanding themselves as their own personalities. And after it they were able to argue about ethics and all. The xenophile/xenophobe conflict is obvious here. MC wanted to liquidate all organics or maybe add them to the hive via cybernetics implants. The free synths seems to preserve the bio-species. But at first, to make that conflict even possible there must be a way for synth to break free from the MC. So there had to be an individualist/collectivist conflict also.
I actualy edited my last reply.
Their not technicaly a hive mind.
Their a communcal machine concenious.
Think like the geth.
Rather than 1 AI controlling all the synths , all the synths poold their minds into creating a concious of the Cybrex. This concious basicaly was a representative democracy as every mind added to the concinous. So if a majorty believed that all organics had to die , the concious would want to wipe out all organic life
For example if all human believes and idea's were pooled into 1 mind.
It would make sense for the initial Cybrex synths to believe to slaugther their inferior biological masters and be free forever. And this changed slowly as Synths are immortal and never die of.
However newer synths that were created as the empire grew might be of a different mind.
Like all democracies they work as long as a majorty agrees on somethings. Chance is big the Ai concenious simply grew to composed of 50% old fashioned cybrex and 50% new fashioned cybrex.
Which probaply caused the 'Communcal machine conceious' to develop a split personality which eventualy caused a civil war.
Where the concious split between militasitic xenofobes and pacificst xenofiles. Looking at their ethos probaply the militaristic attacked the pacifist cybrex.
It would explain that both sides where still a machine concenious since both the evil cybrex and the good cybrex events explain that their smaller ai's still thought to contact the cybrex central hub.
Which tells us both old and new cybrex where still a machine concenious.
The new crisis might be the old Cybrex adpeted warefare knowing that 'non-compliant synths' might disagree in or have conflicting views for the concenious so they probaply just reprogram them all to think like good fanatical purier Cybrex.
Which makes it even more interesting
The entire cybrex line talks about an Ai revolt which was democractic but still militarist and xenofobe.
Where eventualy a civil war broke out where the ?new / old? Authoretharian militirast and xenofobes attacked the new democract / authoritarian? xenofile pacificsts
Where the fanatical purifiers died to the pacificst , who than disarmed and retreated to leave the galaxy in peace and creating many sanctuaries for life only to be wiped out by the very empires they saved by stopping the purifiers and almost having machine guilt not to fight back
Or even to say a revolution? And this contingency is like the CORE from total annihilation?
I think the cybrex are the most interesting
