I completed the main storyline last night, was surprised they gave you that other option. I mean, your whole goal was to save them after all, but I guess they threw that in there to see if you'd do it.
I love everything about the game except the endings, I expected more to happen there. I'll probably try the multiplayer later on then eventually finish everything on the single player. Getting the radio towers, taking over bases, etc.
Also, my PSN is ElCubanoJJC if anyone wants to add me... maybe we could play the coop some time.