Pardon girl taking in shelter (7)
I believe the answer is:
amnesty
'pardon' is the definition.
(I know that amnesty is a more specific form of pardon)
'girl taking in shelter' is the wordplay.
'girl' becomes 'amy'.
'taking in' indicates putting letters inside.
'shelter' becomes 'nest' (I've seen this in other clues).
'amy' enclosing 'nest' is 'AMNESTY'.
(Other definitions for amnesty that I've seen before include "Men stay (anag.)" , "When law is suspended" , "Mass pardon of political kind" , "General pardon, usually political" , "General pardon - international charity" .)