The most common and most likely answer to this crossword clue is the 6 letter word MOSQUE
I've seen this crossword clue in The Guardian
M
O
S
Q
U
E
Buddy explains!

The straight part
We know that "Church" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case church = mosque.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does MOSQUE mean?
MOSQUE noun- A place of worship for Muslims, often having at least one minaret; a masjid.