Chaplain to put up with holy bunch! (3,5)
I believe the answer is:
sky pilot
'chaplain' is the definition.
(sky pilot is a kind of chaplain)
'put up with holy bunch' is the wordplay.
'put up' becomes 'sky' (informal term meaning to throw something skyward).
'with' means one lot of letters go next to another.
'holy' becomes 'pi' (I've seen this in other clues).
'bunch' becomes 'lot' (synonyms).
'sky'+'pi'+'lot'='SKY-PILOT'
'to' is the link.
(Other definitions for sky pilot that I've seen before include "Chaplain (RAF?)" , "Military chaplain" , "refers flippantly to minister" , "leading religious group" , "I'm to drive heavenwards" .)