The new Republic of Ireland manager caused something of a stir when he asked the 42-year-old former skipper to become his assistant, but he is confident Keane will bring huge assets to the set-up.
However, despite the fact the wounds caused by Keane's fall-out with then manager Mick McCarthy and the Football Association of Ireland in Saipan appear to have healed, O'Neill believes his number two got it wrong all those years ago.
O'Neill said: "If you are going back to Saipan, way back in that time, I would have to say that my own view at that time is that I would have disagreed with Roy.
"I would have felt that, having qualified for the World Cup, it doesn't come around too often - for some great players, it has never come at all - and here was this opportunity.
"I thought, regardless of what Roy would have felt about it before, this would be a chance to participate in a World Cup and for a great player, even more so from that viewpoint, so I would have had a disagreement with that."