You could apply decimal point scoring to that game to see who comes out ahead. You would still be using the lineup they submitted, and the one whose players performed better - albeit ever so slightly - would win.
Another idea would be to have each team pick a tie breaker player from the week 17 games. This way they could maybe avoid the teams who may sit players.
I've been in this situation before, and trust me, you will not find yourself here again. Once this happens, you always make sure that there is a system in place to break ties.
Good Luck