I personally wish it ended with L's death. It just seemed so much more satisfying.
Besides, would it kill a mangaka to have the villain win completely in the end?
To quote Berserk Abridged:
hbi2k:But that ending is such a downer...
Zodd: Oh yeah, for you humans. But it's like the only time in the history of anime that the demons win! Every other story ends with the Ancient Hero of Bullshit showing up wielding the legendary Sword of Deus Ex Machina and slicing the hell out of us. Well not this time! This time, WE WIN! Griffith turns evil, everyone gets killed or raped or eaten, fuck you, THE END!