Actually, I think Johns is doing something clever here...
This is Gotham, right? Rendezvous on rooftops are fairly standard, as are mysterious shadowy people suddenly appearing out of nowhere, revealing they've been eavesdropping on you the whole time. At the very least, this is a frequent occurrence for Jim Gordon.
I think a part of the reason why Jim is referring to "Batgirl" and not Barbara directly is because he can't be altogether sure who might be listening right now with all the various criminals and wannabe Batmen running around the rooftops, some of whom are as stealthy as Batman.
As read, I think you can take it that Jim is being clever and referring to past troubles without resorting to "our old friend, Batgirl *wink wink*" lines. Barbara, naturally, is smart enough to pick up on this and tries to comfort her father and reassure him that she is fine, in the face of Jim feeling uneasy over what he no doubt views as one of his greatest failures as a father and a cop; failing to protect his daughter in his own home.
It's subtle but also a damn sight easier to believe than someone as continuity conscious as Geoff Johns not knowing that Jim Gordon has - in numerous stories - either figured out Babs was Batgirl at some point or been told about her secret.
And even if you don't buy the subtext I see, there's nothing in the dialogue to suggest that Jim has no idea Babs was Batgirl - more that he's referring to how he felt when Batgirl disappeared and how powerless he felt then. I think most, if not all, of the recent stories regarding how Jim found out agree that he found out AFTER Barbara was paralyzed.