It's something I've also wondered about; since it's known that several did survive, and they're just the ones where their paths and the player's crossed again, it seems a fair bet that a number of the others managed to get away somehow too, whether by zeppelin, finding another path to high ground or by some other means. Likewise, some of the Sentinel Island NPCs could have survived in theory; the player's dialogue suggests a certain amount of pessimism, though not necessarily certainty. Again, we know at least one of them survived, there may be others.
Of course maybe that's just wishful thinking on my part. But I can open up the developer's console and go back to the unmolested version of Broken Valley any time I want!
