Exiting the subway in New Game Plus
I finally got past the thugs and exited the subway. I didn't have to fight the thugs at all.
First I took out the leader by using the takedown. Next I dropped the smoke and headed to crates. I climbed on the highest crate and used my cryptographic scanner to unlock one set of doors. I threw the freeze grenade a couple of times to trap the thugs and then ran through the door and up the stairs. I jumped over the turnstile and then turned around to see the thugs stuck at the turnstile. I was then able to exit the subway and continue on. I did not get a "you must secure the area to continue" warning so I'm guessing that the developers allowed this escape on purpose.
Watch out for thugs throwing stuff while using the scanner!