well my thougt´s would be that they would destroy the technodrome and leave them to the police or then send them all with the technodrome to some alternate dimension like dimension X and put a time bomb on the dimensional portal so when they would arrive in dimension x it would explode and they couldnt return (or it would take a long time befoore they could)
but in the original comics they probably would kill them
another option that i would prefeer was that they would destroy the technodrome while shredder and krang would still be inside, then they wouldn´t know if they were dead for sure (like in the TMNT 2 game)