In the end, I agree. Its unfortunate. I do think they can re-seed and let the team with the best record play the team with the worst record. While it was deemed unfair that the 106 win Dodgers had to play in a wild card game, its almost just as unfair that the Giants have to play the Dodgers in the first round only because they're the "wild card" team. Giants should get to play the Braves. And Dodgers should have to travel to Milwaukee. In fact I could see this rule shift happening sooner than any of the other ones (the AL playoffs would be the same).
Or each team can schedule 5 (9 inning) day/night doubleheaders. Schedule one of their off days afterwards so they can choose to keep their starters on 4 days rest.
Aren't you putting the warmer teams at a disadvantage by making them play more road games later in the season?