Okay, so I looked into this like a good umpire should, and greymule is 110% correct - I could find no rule that specifically covers this situation, which is actually a bit surprising.
I just got back from calling 3 games tonight, and I asked a number of the other vets on our crew about this scenario. They all said the same thing I said: runner's out, tossed, and if third out, no runners after and including him may score, but the home run may count towards the limit.
Since there is nothing specifically covering this scenario in the rule book, I would have to say that this might have to fall under (cringe cringe) rule 10-1. I *hate* falling back on that rule, but that's what it's there for. It's impossible for ASA (or any ruling body, for that matter) to account for every single thing that can and will happen on a field.
If you agree with me and someday, god forbid, have to make that ruling, you'd better be able to sell your explanation pretty well.
What do others think about this? In this case, I don't think I'm wrong, but being that it's not specifically covered in the rules, that doesn't make me right.