I can't believe any league or any commissioner would consider for a second to change a scoring rule in the middle of the season. If you can't point to it in your current league rules it's not a scoring play. Remember it and amend the rules for next season if you want.
It's obviously a mistake on the commissioner's part in the first place. A clerical error, as one put it. In a league with strangers, I guess you have to leave it. In a league with friends, give the guy his points, ########.
It's an "option" for a reason. Some league may, for whatever reason, choose not to give points for fumbles recovered for TD.
If your commish 'forgot' to check the box, and nobody in the league noticed until week 5, then the league needs to ride it out until end of season.
What if the commish forgot to check the box for passing touchdowns. Would you still be arguing to leave the settings in place for the rest of the season? This is no different.
My opinion:
If your league has written rules and the configuration was wrong then it should be updated, retroactively.
If it was overlooked completely then review in the off-season.
If you want to be "that guy" and force the issue then I think a unanimous decision by all owners should be required to change it now. Some leagues will allow unanimous by all teams not in a matchup containing the player in question. I would vote AGAINST making the change as it could not only change this week's result but also playoff seeding later on.
Full disclosure, I played against JJ today and the TD was not credited to my opponent. He has not complained (that I know of). Even if credited, I would expect Gates to get me the 2 points needed to win tonight so my vote would assume that i win anyway.