Trough offering shelter in church (5)
I believe the answer is:
chute
'trough' is the definition.
(chute is a kind of trough)
'shelter in church' is the wordplay.
'shelter' becomes 'hut' (hut is a kind of shelter).
'in' is an insertion indicator.
'church' becomes 'CE' (abbreviation for Church of England).
'hut' inserted inside 'ce' is 'CHUTE'.
'offering' is the link.
(Other definitions for chute that I've seen before include "Flume" , "Inclined channel for rubbish, laundry etc" , "Sloping trough" , "Slide" , "Waterfall" .)