Mark, a holy man, upset the Magi (6)
I believe the answer is:
stigma
'mark' is the definition.
(synonyms)
'a holy man upset the magi' is the wordplay.
'a holy man' becomes 'st' (abbreviation for saint).
'upset' is an anagram indicator.
'magi' with letters rearranged gives 'igma'.
'st'+'igma'='STIGMA'
(Other definitions for stigma that I've seen before include "Mark of shame or social disgrace" , "Mark of shame, stain on reputation" , "Badge of shame" , "Disgraceful mark" , "Symbol of disgrace or infamy" .)