I say just eliminate the clock stopping on 1st down and be done with the whole thing. No, not directly related to this issue per se, but with the 40 sec clock now, what's the point? Still wait till down marker set for RFP, of course.
Not only would this eliminate these issues, but also with the advent of hurry-up offenses, players are routinely seeing 80 plays or more a game. This would reduce player exposure, cutting over a game's worth of plays over the course of a season without a soul noticing the change.