Omit former church associated with physical training (6)
I believe the answer is:
except
'omit' is the definition.
('except' can be a synonym of 'omit')
'former church associated with physical training' is the wordplay.
'former' becomes 'ex'.
'church' becomes 'ce' (abbreviation for Church of England).
'associated with' is a charade indicator (letters next to each other).
'physical training' becomes 'pt'.
'ex'+'ce'+'pt'='EXCEPT'
(Other definitions for except that I've seen before include "Save for" , "Make a point of not including" , "Other than - saving" , "Exclude, take out" , "Apart from, excluding" .)