To give an update for posterity, as when I was googling this problem I found dozens of other people who had it in the past but gave up without hope: the fix worked!! Thanks again so much plako!
As an aside, we eventually were able to extract the civ passwords from the save, although that didn't actually help, in the end. To find them, I created a hotseat game with 3 players, setting the password to the same thing for each of them, found where the md5 hash for that string was repeated 3 times in the file, and then translated that to the analogous spot in the actual pitboss save. However, that was when our admin remember that he actually played a couple turns for themissing player a few months ago, when the guy went on a business trip, and that his password was a long string of random letters.

(and no, he didn't have that password anymore, as the guy sent it on steam, which doesn't keep logs). So, we couldn't even crack it with rainbow tables. Therefore plako's fix was the only thing that saved the game!