The thing about the idea that Junko influenced Makoto beyond the grave isn't that it's necessarily wrong, but how everyone goes about it is.
No, Makoto wouldn't have nightmares about Junko tormenting him, he wouldn't give her the benefit of the doubt, he wouldn't even remotely think she was ever right.
No no no, what Junko does influence Makoto is keep fighting, succeeding and just being himself now with the added motivation of spite.
She wanted him to Despair? Well now he will Hope harder.
She drowned the world into Despair? Now he will make sure to fix it harder.
She brainwashed people? Well he will just undo it harder.
She wants him to die? Well now he will live on and on.
Hell if she somehow resurrected and tried to died again because she believes she's a mistake that shouldn't exist? Well now he will stop that and try to make her feel better until she doesn't feel so bad.
As long as Junko keeps being Junko Makoto will be Makoto with additional spite fuel.
