Omega, for all intents and purposes, was but a bi-product of the philosophy of complete control X opposed, and but a person made solely to be a weapon in a madman's scheme. Remember, Vile was the true mastermind, Omega simply followed orders. Omega cannot be blamed for the tragedy of Elf Wars as much as Vile can. Promoting Neo Arcadia's ideals Omega would be given a fair trial and under the rule of the kind Master X, retirement for crimes not wholly his own should not be an option.
Furthermore, Omega was originally intended as a weapon to end the irregular war. Without Dr. Vile to guide him, he is a valuable asset for humanity in the fight against irregulars; the ultimate Repliroid, created to be immune to the Sigma Virus, capable of harnessing Dark Elf to its full potential. Omega despite his crimes, is still Neo Arcadian.