Justin,
Punishment, in the legal sense, is different from getting nasty to extract information. Someone commits a crime, goes to trial, and is then convicted, it then becomes necessary to make an example of him to serve as a deterant, as well as remove him from the population for their own safety. That is punishment.
That situation is very different from getting info from a guy because if you don't thousands of innocents will die. You might know someone is guilty but you don't have the time to go through the legal channels to prove it because by the time you do you need bodybags by the busload.
I don't have the slightest problem with Bauer putting a hole in the guy's leg, I'd rather one guy experience pain and a limp than to have an entire city of people dead. You might think of him as collateral damage.