Holy person getting with it at church can be a pain (6)
I believe the answer is:
stitch
'a pain' is the definition.
(stitch is a kind of pain)
'holy person getting with it at church' is the wordplay.
'holy person' becomes 'st' (I've seen this in other clues).
'getting with' means one lot of letters go next to another.
'at' means one lot of letters go next to another.
'church' becomes 'ch' (common abbreviation).
'st'+'it'+'ch'='STITCH'
'can be' is the link.
(Other definitions for stitch that I've seen before include "Use a needle - pain in the side" , "Single loop of needlework" , "in time one could save many" , "Sharp spasm of pain in the side" , "Link, loop or knot made in knitting or sewing" .)