judge, jury, and executioner has certainly been a phrase that has been used to refer to simply punishment and not killing.
http://www.usingenglish.com/reference/idioms/judge+jury+and+executioner.html
It is not exclusively referring to killing. Granted, the general phrase should be "judge, jury, and executor", but that's really the way in which the phrase is used. You're being too literal about it. And if you're going to be literal about it, then why not complain about Batman being a literal judge? Why not complain about him being a literal jury? Seems to me like certain people just
need some reason to decry this movie, and will look to anything to do that.
To help you understand what Roven means, gdw, he's basically saying that, instead of taking these criminals to the police and having them go through the criminal justice system, Batman is deeming them guilty and taking it upon himself to punish them (beating them down and then branding them) instead of letting the system try, convict, and punish them.