I'm all for division winners making the playoffs, I just don't think a division winner should be hosting a playoff game unless their record dictates that. A 5-8 team should not be hosting a playoff game against a 9-4 team (and I know the playoffs don't start to day, but even if the 5th and 6th seed lost their final 3 games, they would both still have a better record than the winner of the NFC South even if said team won its final 3 to finish at 8-8).
I really don't see the issue with seeding by record, but if you wanted to put some more protection on it, you could. Maybe to get a bye you have to be a division winner (so 1 and 2 seeds have to be division winners). Maybe you just keep seeding the same, but the team with the better record is the host of the game (or if the lower seed has a better record, it must be at least 2 games better to host the game if you want a bit more protection on it). That way a 11-5 team would still play at the 10--6 team, but the 11-5 team would host against the 9-7 team.
The NBA saw this as a problem and altered their seeding slightly. The three division winners have to be a top 4 seed, but don't have to be 1, 2, and 3. Additionally, if the 5 seed has a better record than the 4 seed, the 5 seed would get the extra game in the series (i.e. be the home team). I don't see why the NFL can't do something similar.