That sums up my thinking too, though I'll watch for daggum reason. I wondered this at the time (I really did even though I never inhaled the NBA rulebook) but Duncan getting back onto the court when they reviewed to see if Allen's 3 was 3 was illegal and a technical violation. So assuming someone on Miami could have made the FT it may have been over sooner. At the time I thought a Spur had pulled a Weber Fab 5 TO violation.
If the refs didn't stop the game to see if Allen was behind the line(IMO, unnecessary, it looked very clear to me that he was behind the line), the Spurs had 5.2 seconds, could have rushed downcourt, perhaps catch the Heat in a mismatch, or a Heat player late to cover, etc. Popovich looked ready to pop on that, and I agree with him. That seemed to neutralize whatever advantage the Spurs had with possession at that point.