Let's see: would they make someone a Hokage who's only strengths are medicine and strong fists?
Or someone who has achieved Sage mode, has a massive chakra source that's almost unlimited, can control the Kyuubi almost perfectly, and is one of the strongest ninjas alive, who actually strives to be a Hokage so that he can protect his village even better then he does now?
Hm, tough choice. I think they will go with Naruto. Besides everything I mentioned before, he's also the son of the legendary Fourth Hokage. Has Sakura an impressive parentage? Nope.
If they want someone who can protect the village, they are better off with Naruto.