The OP is right, its a lame loophole in the rulebook. The penalty for the extra man is pretty insignificant (5 yards).
The NFL just needs to add one little thing to the rulebook that time will be put on the clock if there is a 12th man penalty with under 1 minute to go.
Edit: As far spiking the ball down the field, the 12 man loophole would work best when a player is tackled on the field (so the QB would either have to spike it or run a play against 12 men, and it would take 6-8 seconds to get lined up to do either and he would have to decide in a split second when he is yelling to other players what to do).
[ Edited by SunDevilNiner79 on Feb 8, 2012 at 9:08 AM ]