Wit upset church more than once (5)
I believe the answer is:
twice
'more than once' is the definition.
(I've seen this before)
'wit upset church' is the wordplay.
'upset' indicates anagramming the letters.
'church' becomes 'CE' (abbreviation for Church of England).
'wit' is an anagram of 'twi'.
'twi'+'ce'='TWICE'
(Other definitions for twice that I've seen before include "Two times" , "You only live -- (film)" , "Doubly" , "Double in quantity" .)