What if humans are to the Ark like the Sentinels are to the Halos? The Sentinels defend the Halo installations from the Flood and whatnot. The reason that they are machines is so that the Flood cannot infect them. Well, to guard the Ark, maybe the Forerunners wanted something a little more 'organic'. Since humans were somehow the 'chosen' race, they put the Ark on our planet, and we've been unknowingly protecting it throughout history. Let's just say the Forerunners stuck us here to guard it in case some whacko wanted to waltz right in and activate the Halos.
So, the Forerunners built the Halos to study the Flood and eliminate the Flood threat if they leave the rings. They also built a safe-haven on Earth (protected by humans) to protect them from that blast. Then why are they mysteriously gone? Maybe the Flood was released by an overzealous individual (343 Guilty Spark?) and things got bad, fast. They had no time to evacuate and decided to activate the Halos, leaving the Ark and humans on Earth unaffected and isolated.
To each their higher purpose.