At church, note, a reformed spy is just a human soul (6)
I believe the answer is:
psyche
'a human soul' is the definition.
(I've seen this before)
'at church note a reformed spy' is the wordplay.
'at' says to put letters next to each other.
'church' becomes 'ch' (common abbreviation).
'note' becomes 'e' (musical note).
'a reformed' indicates an anagram.
'spy' with letters rearranged gives 'psy'.
'ch'+'e'='che'
'che' put after 'psy' is 'PSYCHE'.
'is just' acts as a link.
I am not very happy about this link. Some or all of it may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for psyche that I've seen before include "Human mind or soul" , "The beloved of Eros" , "Sole and spirit" , "Core of one's personality" , "Inner self" .)