Oh, and why would they even try to kill Ganondorf if they could just send him straight to the afterlife anyway? He's gonna end up there one way or another (according to you) and if they can avoid trying to kill him for fear of it not working then why wouldn't they just send him straight there anyway? It's not the afterlife. It would have been made clear or at least hinted to if it was....which it wasn't.
And if I recall, only the Twili call the Twilight Realm the Twilight Realm, perhaps the people of Hyrule know it by a different name. For instance, Auru calls it the underworld(now if that isn't a name for the afterlife, I don't know what is. Well actually I do, but you get the point). And Midna states that some people call it a Realm of Shadows.
OMG SHE CALLS IT THE REALM OF SHADOWS!? Correct me if I'm wrong (and I'm not), but don't many of the monsters in the Twilight Realm resemble shadow-like creatures? The birds look like extremely dark, shadowy birds. The monsters you fight on land look like shadow creatures. There are even little shadow balls that you fight.
Also, someone calling it the underworld doesn't make it the underworld. Many people come up with their own names or analogies for things they don't understand. Oh, and I'm pretty sure that Zelda calls it the Twilight Realm. Based on the beginning of the game, no one knows it exists except for Midna. It's a well kept secret probably so no one tries entering it because Ganondorf is there.
You can argue this all you want but there is absolutely no solid evidence at all for it being the after life.
It's a prison/home for people who once committed bad deeds. It's not meant to be looked into any further.