Section of thesis (emended) returned as punishment (7)
I believe the answer is:
nemesis
'punishment' is the definition.
(thesaurus)
'section of thesis emended returned' is the wordplay.
'section of' indicates the answer is hidden within the clue.
'returned' says the letters should be written in reverse.
'sisemen' can be found hidden inside 'thesis emended'.
'sisemen' reversed gives 'NEMESIS'.
'as' acts as a link.
(Other definitions for nemesis that I've seen before include "Siemens (anag.)" , "Goddess of revenge - seems in (anag)" , "Divinity" , "causes downfall" , "E'en miss (anag.)" .)