I think a more apt analogy would be what's scarier - a single socipathic killer or an endless hoard of big hungry bears.
The flood being a mindless disease seems scarier to me because it's something that can't be reasoned with and doesn't follow any kind of true pattern or have any real goals - it's essentially chaos incarnate. It also introduces the question of what will intelligent people attempt to do in order to stop the mindless disease (like building giant super weapons that will kill anything within thousands of light years). Plus the Flood in Halo 1 were a bit of fresh air compared to the Humans vs Covenant - who were both kind of operating under their "higher motivations" idealogy already.
Ah, but the Gravemind cannot be reasoned with. It is intelligence without morality, qualms, or indecisiveness. It simply
is, in a way that is difficult to wrap one's head around. This is a being that will absorb, subvert, and kill everything in its path, wreaking unthinkable destruction in the name of a cause we can't even begin to understand.
Having the Flood be an unthinking parasite makes them more relatable, in a way; they're the plague, but with (comparatively) gigantic bacteria. The Gravemind makes them something entirely alien, and, in my opinion, much scarier.
Granted, this is all undermined by the fact that he looks (looked) like Audrey, but nonetheless, I loved the concept. Plus, no Gravemind means no Logic Plague, and that'd be a damn shame. Such a cool idea.