Makes amends for throwing a stone (6)
I believe the answer is:
atones
'makes amends' is the definition.
(I've seen this before)
'throwing a stone' is the wordplay.
'throwing' indicates an anagram (letters get thrown around).
'a'+'stone'='astone'
'astone' is an anagram of 'ATONES'.
'for' is the link.
(Other definitions for atones that I've seen before include "Makes amends for sin" , "Makes up for injury or offence" , "Makes up for, say sin" , "Makes redress" , "Makes reparation" .)