yeah the big debate has always been does Gordon know? Now we all knew he always knew Barbara was batgirl.
i believe there is a scene in another book where batman says Jim Gordon is too good a detective not to know who Batman is. (its a conversation with superman where he discusses that he thinks that Perry is too good a reporter to not know who superman really is.)
they discuss that both pretty much choose to ignore what they know or choose not to seek out concrete proof.
i mean, if your daughter is swinging around in a cape and cowl with another guy, YOU WANT to know who that guy is.