"First of all, there’s zero evidence this offense has had any rhythm all season long that would be disrupted by one play or series."
Come on with this. It sure doesn't help with rhythm. 
I'm not blaming him, but in the last 2 games, Howard has been sent out by the staff cold and given up a 10 point swing. Sure, our offense may have punted on those possessions if not for the interceptions. Lunch may have thrown a pick. But, those drives gave USM a TD lead instead of 3 at the half and swung momentum. It also tied the game for Troy and they took the momentum.
Yes, this even with all with the injuries. Can't be discounted. However, you can't say that too much is being made out of those decisions. UL players even came out a few years ago saying that when you put in a new QB, simple stuff like the spiral make a difference catching a football. Ball placement. Left-handed vs. right-handed. A drop that could be a catch hurts the rhythm. 
There are countless examples of the Des tenure were rotating 2 QBs (outside of 1 play short yardage) has backfired. We kill our own momentum when we get it and that does not help with injuries and all the other stuff that are reasons this team is struggling.