No matter what Neal would think when he got hold of the transcript (and Clinton was under no illusion that Neal somehow would, closed meeting or not), he was not overcompensating in the face of arguable favoritism.
Truthfully, Clinton wanted - needed - to believe that reform was possible. The system could work, and maybe it had. Maybe Neal had changed, maybe the change went deeper than a surface gloss reflecting the desires of those around him. God, he hoped so.
But justice wasn't just about reformation; it was also about the victims. Sure, the only crime Neal had been successfully prosecuted for had been against a faceless, insured corporation, but that didn't mean there weren't victims, there and in the other cons before and since, ones Neal had never copped to and never would beyond the broadest hints. Wink-nudge-see-how-clever-I-am. Crimes he would never atone for, not really.
So, no. Clinton wouldn't pretend the attraction didn't feed into his statement. He knew he did hold people he... cared about to higher standards. But it wasn't the whole story. Neal ought to serve out his sentence, the only one he'd ever serve. It might only be an approximation of justice, but Clinton needed the gesture at least.