Factual error: When Clark speaks to Jor-El for the first time in the Fortress, Jor-El says "I will have been dead for many thousands of your years..." Fine in theory - Baby Kal-El travelled to Earth at above light speed so time passed differently for him. However, as such, wouldn't Jor-El have seen Earth as it was thousands of years ago? Which also makes there a problem with all the things Kal-El was taught during his voyage to Earth, as Jor-El references Einstein by name, for instance, and he would not have existed at the point when Jor-El sent him to Earth.
Factual error: When Superman is turning back time by flying around the Earth, right before he starts orbiting the Earth is spinning way faster than it actually should be. If the Earth actually spun that fast, a day would pass by every 1.44 minutes.
Answer: There are generally two methods of time travel. Skip vs Slide. When you slide through time, you are in essence rewinding or fast forwarding a tape. Time will accelerate to the desired moment. This method, the traveler will witness the rewind and will only allow one of them to exist. When skipping, you are plucking yourself from the time stream and placing yourself in the desired moment. This method, travel is instantaneous and can allow for multiples of the traveler to exist at once. Superman rewound time. He used the slide method and went directly to Lois after doing so. This means those he previously saved...died after his reversal.
Or he could have used the skip method. Like you said, it enables a traveler to pluck themself from the time stream and placing them at the desired moment allowing for two Supermen to be able to prevent both missiles from reaching their destinations.
He couldn't have used the skip method if he rewound time.
Bishop73