I think they need to develop his character much more thoroughly. The reason I like him, is because he has potential. The only "anti-hero" we've really seen has been Axel (and no I don't mean Lea). Vanitas's story from the novel should be canon, it would give him more personality and perhaps we'd even feel bad for him. He would make for a great anti-hero. Perhaps one minute he could inadvertently help Sora and the gang, but saying something along the lines of: "I didn't do that for you, I have my reasons." and then he disappears into a corridor of darkness.
I don't know...too much potential to just kill him off. He was never truly loyal to Xehanort anyways, he really only seeked his own salvation: to forge the x-Blade. We saw he was just fine betraying his master/creator.