Church council’s case for Sunday: sign of agreement follows (5)
I believe the answer is:
synod
'church council's' is the definition.
(type of church assembly)
'case for sunday sign of agreement follows' is the wordplay.
'case for' suggests removing the centre (the letters which encase the others are used).
'sign of agreement' becomes 'nod' (a nod can indicate agreement).
'follows' says to put letters next to each other.
'sunday' with its middle taken out is 'sy'.
'sy'+'nod'='SYNOD'
(Other definitions for synod that I've seen before include "Clerical assembly" , "Ecclesiastical gathering" , "Ecclesiastical council" , "Ecclesiastical assembly" , "council meeting" .)