NFL coaches hate Thursday night games, because their players have essentially only half the preparation and recovery time as they do on a normal Sunday game schedule.
So here is my (partial) solution. Where possible, teams playing Thursday night should have their bye week the previous weekend. For teams with the bye week the previous week, a Thursday night game is no issue -- in fact, it might even be a benefit, breaking up a single long-preparation period between games into two longer-than-average periods.
This is probably only a partial solution. Only 8 weeks have bye weeks, and since for week 1 the Thursday game is no issue, this only solves the Thursday problem on 9 of the 17 regular season weeks. I suppose we could extend by weeks to more weeks of the season, but even as they exist today a partial solution is better than none at all, right?