I think that you should go with the rules that you have in place, and absent a firm rule, you have to go with precedent. If you started the season with a precedent of giving the Toilet Bowl Champ #1 overall, you have to do that again this season. Never change horses in mid-stream.
That said, have any dissatisfied owners propose that rule change for next season and put it to a league vote. We usually have a voting session before the draft starts to cover any rule changes, with discussion and lobbying for a few weeks prior.
We have considered adopting a "draft" for draft position - Toilet Bowl gets 1st crack at their choice of draft slot, Super Bowl Champ gets last. It isn't unfair, provided the owners have elected to use this system.
If you are stuck with the Toilet Bowl champ getting #1 overall and he doesn't want it, she has the option to trade down if they believe it will be beneficial to do so. Every owner values the various draft slots differently. Surely someone will be interested in the #1 overall.