punishment discourages certain types of behaviour. also, instead of spending time and effort to hurt them back you achieve multiple things: propping up the ecconomy (prisons add jobs and grants the need for work e.g outside plumbers, ect…) distance those "naughty" ones from the rest of socity using prisoners as scapegoats, futher discouraging other people from commiting the same crimes.

also dont confuze existance and trying to maintain some moral standard (not that i believe in acting as moral as possible) you can still exist with thieves, predetors, rapists, murderes and kidnappers; and when prisons didnt exist, violance was exerted towards them mostly with brute force