Right, if you can't stop the clock in the last 2 minutes, it just means you better start running your 2-minute offense a little sooner.
With that said, I would not mind this change. I would get rid of all timeouts and have a rule that says the clock stops after every play in the last minute only. This would be true regardless of whether the offense is ahead or behind. If the offense is ahead, they can not simply kneel down to end the game. If the offense is behind, they will have a chance to score without needing to call time-outs or get out of bounds.