Classified as revolutionary church in organised protest (3,6)
I believe the answer is:
top secret
'classified' is the definition.
(I've seen this before)
'revolutionary church in organised protest' is the wordplay.
'revolutionary' says the letters should be written backwards.
'church' becomes 'CE' (abbreviation for Church of England).
'in' is an insertion indicator.
'organised' indicates anagramming the letters.
'ce' back-to-front is 'ec'.
'protest' is an anagram of 'topsret'.
'ec' going into 'topsret' is 'TOP-SECRET'.
'as' acts as a link.
(Other definitions for top secret that I've seen before include "Erect post (anag)" , "visible to hardly anyone?" , "As 007 mission" , "As Bond mission" , "Well-hidden" .)