Penetrate jetty alongside church (6)
I believe the answer is:
pierce
'penetrate' is the definition.
(I know that pierce is a more specific form of the action penetrate)
'jetty alongside church' is the wordplay.
'jetty' becomes 'pier' (I've seen this before).
'alongside' means one lot of letters go next to another.
'church' becomes 'CE' (Church of England).
'pier'+'ce'='PIERCE'
(Other definitions for pierce that I've seen before include "Make hole in with sharp object" , "Make hole in with something sharp" , "Perforate" , "cut to the quick" , "force way through" .)