Thanks for the feedback from everyone. It appears that we've come to an agreement to just forfeit the rest of their games, turn their 4 wins into losses (they are currently 4-30), and move on. A concern was brought up to me that if there is a 1 game difference to decide who gets into the playoffs, one team could benefit from this. Well, with how MLB scheduling works, every team in the NL East will have played the same amount of series against the Nationals (6 CC games), and the other teams in the NL will have played the same amount of series against the Nationals (2, 1 home and 1 away). Everybody gets credited with the same amount of wins.
So, the only issue where this could come into play is with interleague play. According to the schedule, the Nationals have played 1 CC game against the Blue Jays, 2 games against the Orioles, 1 against the Red Sox, 1 against the Yankees, and 1 against the Rays. All of these games have already concluded and they lost all of them, so nothing will be affected by these changes.
The only way any issue could arise is if one of the teams they beat (Reds, Pirates, Mets, Phillies) happens to get in to the playoffs by 1 game (the loss I am now changing to a win), and the team that was left out was not awarded any "free wins". If that happens, I will conduct a 1 game playoff between the two contending teams on a random map, winner goes to the playoffs. The alternative is to keep those 4 losses as on the books, but with me giving several teams "free wins", the same situation would arise just in the inverse. So, I think this is about as fair as I can make it.
Sound good to everyone? I will also post this in the tourney thread should you need to reference it in the future.