One of the few things I liked about the "liberties" taken with the setting in Fallout 2 was the ghoul city running the nuke plant. Clearly demonstrated the kind of situation where ghouls could openly coexist; they pipe power to the humans working in a high-radiation environment, humans provde protection in return. Super-mutant miners was another reasonable idea. In the rare (and it should be rare, though I wouldn't expect Vault City's genocidal tendencies to be the norm) cases of coexistance, that kind of division-of-labor and thus necessity-of-coexistance should exist.
Please excuse me if I seem confused but the "Great Leader" of Vault City wanted you to destory the Power Plant and the Ghouls living around the plant. It was your choice as what to do, and I hope in everyone's kind heart they showed a little mercy kept the ghouls alive and recruited Henry at least for a little time. It was your choice to fix the plant.
Might I add the supermutants were very unintelligent and their commander was the exception to the mutants. I think the Vats of goo might have fried their brains but they were no smarter than the deathclaws in FOT and FO2. As long as there are people like Vault City's leader who want to kill the ghouls and the Brotherhood who want to kill the mutants, there is no way that super mutants or ghouls will co-exist with the human survivors.
I'm sorry but maybe in a perfect world, but not in the post-apocolyptic world.