Milo is the alt-right leader in the same way Pepe is their pet mascot; he doesn't align with them at all, he only aligns with Annoying Orange, what the alt-right did was they adopted him as their leader without asking him and now he just kind of is their leader.
The alt-right won't die because of this. It's a Kekistani cult founded and dwelling on the internet. They're going to be fine.