Is prayer held by theologian to be badly out of favour? (9)
I believe the answer is:
disgraced
'be badly out of favour?' is the definition.
'is prayer held by theologian' is the wordplay.
'prayer' becomes 'grace' (grace is a kind of prayer).
'held by' means one lot of letters goes inside another.
'theologian' becomes 'dd' (Doctor of Divinity degree).
'is'+'grace'='isgrace'
'isgrace' inserted within 'dd' is 'DISGRACED'.
'to' acts as a link.
(Other definitions for disgraced that I've seen before include "Shamed, dishonoured" , "Suffering shame" , "In the doghouse?" .)