Thanks Mr Death. I will admit that likely means a set of bones was found, and in all probability was Justin. Even if Justin had a spare skeleton or two lying around I am sure the White Council could tell one from another if they really wanted to. Worth remembering that many on the Council knew who Harry was, and was meant to be before he joined the Council. We still don't know many details apart from the fact he is a "Starborn" whatever that means. So likely the White Council took a special interest in a Starborn breaking the laws.
I do think that it doesn't rule out Justin being active from beyond the grave, post-death if you will. Whether as a Ghost, resurrected human or body switch or some other spooky thing. But it likely rules out him flat out surviving the duel.
In saying all that - a fair few things in those early books had not been ironed out and have been retconned or contradicted since (both large and small details). Hopefully Jim reveals it before the BAT.