Separate church finally accepted in diocese (6)
I believe the answer is:
secede
'separate' is the definition.
(seceding is a kind of separating)
'church finally accepted in diocese' is the wordplay.
'church' becomes 'ce' (abbreviation for Church of England).
'finally' suggests the final letters.
'in' means one lot of letters goes inside another.
'diocese' becomes 'see' (I've seen this before).
The final letter of 'accepted' is 'd'.
'ce'+'d'='ced'
'ced' going inside 'see' is 'SECEDE'.
(Other definitions for secede that I've seen before include "'Withdraw formally, from a political body perhaps (6)'" , "Withdraw (from organization)" , "Withdraw from a political federation" , "Disaffiliate" , "'Withdraw, break away (6)'" .)