The Punisher did say they were "thieves and killers," meaning they were more "regular" bad guys instead of just being against the Registration Act.
The Fraction story was more like the Punisher telling Captain America "This is what you WANTED me to do, so don't pretend otherwise." Of course, I doubt this was remotely what Cap had in mind. BUT... What Frank was saying wouldn't bother Cap so much if it wasn't a little bit right.