Jor-El does tell him, during the journey, I believe, not to interfere in Earth's history. You can take that as Jor-El knowing Kal-El would have have the ability to turn back time, or you could take that as he shouldn't run for president. It's up to you. Movie makes more sense if you believe it to be the former.
Or Kryptonians are sooooooo advanced they cracked the method to time travel. Jor-El probably imparted the method to Clark during his training.