(Yes, I know, I do plan on blogging about ColdFusion, at some point, really, but I'm just a tiny bit addicted to LOST. Just a reminder to my readers - if the OT stuff bugs you, you can filter by category when you view the blog. :)
First off - the whispers seem almost casual. I.e., they aren't statements of some kind of god-like entity "We shall destroy them!", but the kind of thing you would expect people to say. In fact, there even seems to be some in-fighting between the voices in the whispers:
Maybe we should just talk to him
Man's voice: No if he see us it will ruin everything
The voices seem to be from people observing the characters and commenting on their actions.
Here is a crazy idea (and why not, LOST likes to generate crazy ideas). We know an experiment went wrong. What if some kind of experiment sent the test subjects to the "Other Side"? Not dead - but just... away. These people have the power to influence the real world - with visions and other manifestations. The Beast could be one of them - and could represent someone's anger at being sent away. From the whispers it is apparent there are different people involved - and while they don't seem evil, some certainly could be. In fact - the term LOST could not be referring to the guys on the plane - but the poor souls lost in the experiment. In fact, the Others could simply be trying to save these folks - and in fact aren't really bad guys per se, just desperate to save their friends. We know Walt is still alive, so they didn't murder him. Maybe they think they can use him to help save the Lost?