Separate Church denomination's leader in diocese (6)
I believe the answer is:
secede
'separate' is the definition.
(seceding is a kind of separating)
'church denomination's leader in diocese' is the wordplay.
'church' becomes 'CE' (Church of England).
'leader' indicates taking the first letters.
'in' is an insertion indicator.
'diocese' becomes 'see' (I've seen this in another clue).
The initial letter of 'denominations' is 'd'.
'ce'+'d'='ced'
'ced' inserted within 'see' is 'SECEDE'.
(Other definitions for secede that I've seen before include "Withdraw formally from membership of an organisation" , "'Withdraw formally, from a political body perhaps (6)'" , "'Withdraw, break away (6)'" , "Withdraw from a political federation" , "Withdraw (from organization)" .)