I don't think anyone is under the delusion that Sheng Jue is a good guy, the man literally snatches bodies, and practices cultivation arts that require the death and refinement of numerous people.
The few reasons why most people don't find it to be an issue is because the body he has snatched is that of one of our worst enemies or a stranger depending on choices, and at the very least hasn't attacked us at present. Plus with so few sources of cultivation know how outside of the existing factions, his involvement is needed to progress especially if our character is to acquire strength outside of our factions scope.