I keep fighting them, but it seems like they would eventually stop spawning when there aren't any more people to turn into Cie'th unless the people respawn. I'm wondering whether it would be worth it to slow down and try to eliminate them all or if I should just try to get past as many as possible. Do they keep coming, or can I kill everyone eventually?
No, you cannot kill everyone. They will eventually respawn, and seeing as the cp rewards you get for them are almost non-existent, you are better off passing them by as fast as possible.
However, the Ghouls make one of the better opponents for farming Potent Drops just because they are so weak. Although I do recommend a Collector's Catalog because the drop rate is fairly low.