Gordon might be talking more of a general "feeling" at the time than whatever he knew.
BATMAN CHRONICLES #1 had Jim Gordon and the Huntress stopping some hijackers on an El-Train. Gordon narrates most of the story, and says that he found out Barbara was Batgirl by finding her costume *after* the Joker shot her.
"I never told her. I never wanted to admit it to myself. But I found the mask and cape among her things. And there was no lying to myself anymore."
To clinch it, at the end of the story, Batman tells Gordon regarding Huntress: "You're not the only one she reminds of Barbara."