There is another purpose to this rule besides lapped cars being mixed up between the leaders.
Consider this example:
We are in the 2nd half of the race. Two drivers (let's say, Hulkenberg and Perez) fight for P10, which is effectively a fight for a Championship point. They are far from the leader (almost a lap down). Perez is currently P11 and a few seconds behind Hulkenberg, who is P10. Perez is lapping a second a lap faster than Hulkenberg and so he's almost sure to catch Hulkenberg and overtake him before the end of the race.
The race leader catches up to Perez, who gets shown blue flags and lets the leader pass him. He is now lapped. At this moment, some accident happens and the safety car is deployed. It picks up the leader and other drivers line up behind him, including Perez, who's been lapped just before the safety car was deployed and so he's right behind the race leader. But Hulkenberg hasn't yet been lapped and so he is now allowed to do an entire lap and join the end of the queue behind the safety car. Now Hulkenberg effectively has entire lap's advantage over Perez (even though it was just a few seconds before the safety car period) and Perez will not be able to close that gap.
However, if the lapped cars are able to unlap themselves, Perez will also do an extra lap and join the queue just behind Hulkenberg, which means he will be able to fight Hulkenberg for 10th position.