Oh... I got mistaken on the order of events. You don't need to return to Goug with the new stone if Cloud is already released -- he'll show up in Zarghidas after Igros. For some reason you do need to clear that series of fights. No wonder you didn't quite figure this one out. That's a stupid flag since there's no indication it changes things.
Some people interpret the ending as Olan hallucinating and Ramza/Alma actually being dead. I like this ending more (since like you, I think it's more powerful if they end up dead), but there's nothing really to support it. The argument is that Balmafula doesn't acknowledge them, but she doesn't say anything through the cutscene anyway (which has led some people to claim that her tongue got slit by Delita when he came upon her earlier). It's... not a very strong argument.
If they're alive, people generally say they escaped by using the stones. Somewhere the game says that when all 12 stones are together a miracle can occur, so that leads to possibilities.
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No amount of planning will ever replace dumb luck.