Is a substitute to put up with transgression? (6,2)
I believe the answer is:
stands in
'is a substitute' is the definition.
'put up with transgression?' is the wordplay.
'put up' becomes 'stand' (to put with something is to stand or endure it).
'with' says to put letters next to each other.
'transgression?' becomes 'sin' (sin is a kind of transgression).
'stand'+'sin'='STANDS IN'
'to' is the link.
(Other definitions for stands in that I've seen before include "acts for the moment" , "deputy" , "Deputises" , "Acts as a substitute" , "Acts as sub" .)