Rare blemish on church (6)
I believe the answer is:
scarce
'rare' is the definition.
('scarce' can be similar in meaning to 'rare')
'blemish on church' is the wordplay.
'blemish' becomes 'scar' (scarring is a kind of blemishing**).
'on' is a charade indicator (letters next to each other).
'church' becomes 'ce' (abbreviation for Church of England).
'scar'+'ce'='SCARCE'
(Other definitions for scarce that I've seen before include "Common? Definitely not" , "Hard to get" , "Scant, meagre" , "Like gold dust" , "Not plentiful, in short supply" .)