The empire's failure was to neglect the protection of the stone. If they didn't want to bother with it, they should have found a way to relocate it elsewhere. An outsider stealing it wouldn't necessarily care one bit how it affects the empire, which is exactly what happened.
I hope when John Doe gets offed, the spirit gives them a split body as a member of their army as a token of gratitude. Would be neat, and it would make sense for MC to try to get more powerful members who aren't demon/undead, considering all the holy-aligned stuff the will of the world's throwing at them.