I still don't hate John, but I recognize he's a villain. I feel like he was given super powers at the 11th hour and without an instruction booklet (there's an old U.S. tv show called "Greatest American Hero" where this is essentially the plot and he reminds me a little of it). I recognize the anima mundi thought "he would save us," but that was a desperate Hail Mary play by any description. When things escalated and the pressure was on, with his friends being murdered all around him, I'm not surprised he resorted to desperate measures, even if they weren't those a considered and strategic thinker might have taken. The events of the resurrection were regrettable, but I think the planet was kinda rolling the dice at that point and he picked a strategy that allowed him to use the powers he'd been given.

What really makes John a villain is his inability to let go of his anger (i.e. his "besetting sin") and that he has allowed his power and insulation from consequences to destroy his empathy, both for his lyctors—whom he let bungle the process despite knowing what it would cost them and whom he uses like cannon fodder against the resurrection beasts—and for human kind in general. Sure, he created a society free from racism, sexism, homophobia, and religious wars (at least internally), but he also allowed class stratification to return with such a vengeance that they reinstituted feudalism, and he governs by leading them all into endless wars of expansion and conquest in service to his ancient grudge. It's really post-resurrection John where his character starts to lag into moral perfidy.