Utopia justifies the Means. Since the overall concept of Krellian's plan and the world of Xenogears itself is based on Gnostic beliefs, the people who went with Krellian are debatably better than off than Fei's group. Course Fei's own story is kind of a rejection of Gnostic and even Buddhist thought.

I never really saw Krelian as evil or even a villain. Manipulative bastard at times? Sure, but he was always a lesser evil compared to just about everyone else on the villains side that weren't Ramsus and the Emperor.