This is a tough situation.
Your commish sounds like a decent guy, and it isn't like he benefitted greatly from having Dye in the lineup as it's not like he went off or anything like that, like you said.
I like the fact that your commish gave you the explanation and didn't run away from your e-mail or do any of the other stupid things that we've heard of other commishes doing through these forums.
I think this is what you need to do...
E-mail the commish back and ask him to make this situation public to the rest of the league. Have him explain what he did, why he did it, and all that. Along with that, have him promise the league that he will never do that again, no matter what the situation, in order to maintain his integrity as a commish and the integrity of the league.
Furthermore, I believe the league should vot whether or not he gets to keep Dye's stats from that day. The league may allow him to keep the stats because Dye didn't go nuts that night, or they may ask him to revert back to having Beltran in his lineup. Either way, the league should vote.
Other than that, if he's willing to do those two things and it satisfies the rest of the league, I say you're good to move forward with the season. If the situation is as simple as his reply to you describes he should have no problem bringing it forward to the league, correcting it as it is deemed fit, and move on.
Just my 2 cents.