Still thinking about this, LOL, and I'm pretty convinced now that the two cops that Gordon are referring to are Davis and Polk, the cops at the hospital that Joker killed.
Nobody knew that Joker was at the hospital to begin with, except for Harvey and the people who were taken hostage, and by the time they were freed, Gordon was long gone. Wuertz had that day off, and the only person at the bar, as far as we can see, is the bartender, whom Harvey could have subdued. He let Ramirez live, but Gordon was probably with the SWAT team at the Pruitt building already, so nobody would have missed her absence until later.
I'm trying to remember whether there was another bodyguard in Maroni's car besides the driver. Harvey pulls one away when some guy is helping Maroni into the car, but in the next cut, it seems like Maroni just closed the car door and the car's already going. It doesn't seem to be enough time for the driver to walk to the other side of the car, get in, and start driving.
Clearly I need to see this again.