I applaud the spirit of your story but not sure I agree it's possible to repair spirit without belief in some form of higher identity.
If any higher identity or authority has been wronged, it's nature.
Dont we need to have some faith in nature, to have a foundation for spirituality?
An author who seems to have his finger on the pulse of spirituality, imho, though I am no expert on the subject (It's all subjective, though it does follow logic, I guess), is David Price.
I'd definitely recommend his books and Medium stories to anyone.