Not that I'm surprised that this has already drifted off-topic, but this earlier point needs re-emphasizing:
Furthermore, we're actually there to protect Japan to some degree: their own military is pretty limited, as required by Post-WW2 treaty. In recent years, they've been able to project a bit more power, but with a neighbor like the DPRK, I'm sure the Japanese government appreciates having some backup. But, as the article points out, a lot of the locals are less enthusiastic about the whole thing, making the issue more difficult...
As it stands, via post-WWII treaty, Japan cannot maintain a full-fledged standing military, nor can it undertake military action outside of its own borders (which is why people made such a big stink about the Japanese unit that was
stationed in Iraq). This is why Japan's military is known as the Self-Defense Force, as it's limited to domestic actions. Currently, Japan relies on the US military for external actions and practical defense, and short of said treaty being revised, this will continue to be the status quo. So long as the Glorious Psychotic Leader remains in power in North Korea (though Hugo Chavez seems to be gunning for that title himself), the Japanese government essentially
needs Okinawa (unless that shift to Guam Bobboau touched on is true), and I can't see them taking any serious steps to close it, no matter what public outcry may desire.