That aside, in my opinion (the rational one at least) Gon and Killua needed a separation after all that's happened in the Chemira Ant Arc. Their friendship has become unhealthy, esp. to Killua.
Killua, due to his upbringing, self doubt and lack of trust in people, developed a selfless over-protective sense to those he cherishes and does trust. He wanted to protect Gon's innocence but failed and it broke him. I understand leaving Gon's side would do better for him in finding and thinking more about himself, but I can't see how Alluka at his side would help. I kinda feel like he's left one precious friend he sacrificed all of himself for, to do the same thing for two; Alluka and Nanika.
In the end, it is how Togashi chose to do it and he sure isn't predictable. He still can fix things at a later stage, we know nothing. I just hope Killua won't pull a Kurapika and go off-screen for ages, and if he's shown, I really hope Alluka wouldn't stay so one-note in terms of character and story.