Blemish by church rarely seen (6)
I believe the answer is:
scarce
'rarely seen' is the definition.
(I've seen this before)
'blemish by church' is the wordplay.
'blemish' becomes 'scar' (scarring is a kind of blemishing**).
'by' 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 "Deficient in quantity" , "exceptional" , "Not plentiful, in short supply" , "Hard to get" , "Like gold dust" .)