Two things determine the fairness here: Waiver rules and precedent.
What are the waiver rules? I assume dropping a player must lock the player for a period of time to allow waiver claims to be made. If not, he would have just immediately drop/add again to fix it. If he used his Commish power just to avoid a drop/add fee or some type of waiver penalty, then I think that is little underhanded.
Which brings us to precedent. He said he would have done that for any owner who made a mistake. Really? Has that ever happened Is there a precedent set on how long a "mistake" can go before notifying the Commish? It's a very gray area, so if it isn't in the rules and it really is just at the Commish's discretion, I hope this isn't the first time it has occurred. If so, you can either fight him, or because the move is somewhat meaningless (comparative to other players that could have been involved) you could just let it go but write it down so next time someone "makes a mistake", you ensure the same rules are followed.