Joe, you're right that it couldn't have been Lee that long after the war, as he died in 1870.
I, too, have read several stories of Lee making that statement to Stockdale at that meeting. And it was indeed after the meeting was over that he said it.
This meeting was actually set up by Unionists to help show that the South was wrong in their "efforts" to secede. Lee, having been invited in the hopes he would speak on behalf of the South, quickly realized the meeting was an attempt to actually demonize the South, he refused to speak publicly.
Paraphrasing Lee: If I had known the South would be treated in this way, I would never have surrendered at Appomattox. No sir, not in a thousand years.
Lee was appalled at how the Union treated Southerners after the war and felt he was powerless to stop it.
Another great book about Lee is
Reading The Man: A Portrait of Robert E. Lee Through His Private Letters, by Elizabeth Brown Pryor, (2007). Ga.windbreak also has a copy and can attest to how revealing this book is about Lee's feelings on many subjects, including the surrender. All through his own personal correspondence.
I think the whole thing boils down to the North being jealous that Robert E. Lee fought for the Confederacy and not the Union.

JMO
SBG