My past experience tells me that games with weird rules like this usually turn out to be horribly broken. The only reason my fourth game (MoonWolf) worked is because I gave up on the really weird rules and set it up more like a normal Werewolf game. Turns out, the people who've been playing and refining the standard version of Werewolf know what they're doing.
The problem with the nickname idea in particular is that there's no way to tell beforehand who you're actually going to hit- basically, all the targets would be randomized. The wolves would be able to share their nicknames and thus keep from murderizing themselves, but the villagers would have absolutely no idea. It'd be horribly wolfsided (and no, reducing the number of wolves at the start is not an effective way to balance that, as evidenced by the last game as well as both of my TarkirWolf games).
Giving each player a few accurate realname-nickname pairs at the start of the game might give the town enough information to work with, so they can share it and actually lynch who they want to lynch. Maybe.
What might work better would be to permit lynching of players by their real name, but require that all night actions be targeted by nickname. So the town could lynch whoever they please, but night actions would still be befuddled. Might work if enough (read: most, if not all) players have abilities that help them match nicknames up with real names.
