are you talking about the hole in the little bridge that connects the chain stays right behind the bottom bracket shell? i would put some naval jelly around it for five minutes, then wipe it clean. you might do this on the bottom of the frame first to ensure it won't goof the paint. if you overhaul the bike completely, that would be your best chance to spray some boeshield in the tubing and tip the bike all around allowing the protectant to coat the steel and help prevent any further rusting.

if there's rust there, you're likely to have more in the inside of the bb shell that you can clean with wd-40 and a brush or scouring pad.