You're one hundred percent right about Japan wanting us there. The central government is unable to field their own offense capabilities and despite having a sizable Self Defense Force they aren't anywhere near as prepared for war as the US is. That being said, this isn't about whether or not the US should be in Japan. 
The issue with Okinawa is a separate issue. One that dates back to Japan's forced occupation in 1606 by the Satsuma and the eventual annexation in 1879. This was followed by forced assimilation and the dismantling of the once Ryukyuan culture by the Japanese. The real culprit here isn't the US, but the Japanese government. They sacrificed Okinawa in World War 2 and again in the aftermath with ignoring the rights granted to the people by Article 95. Whenever the proposal of a new base is leaked communities around Japan put a stop to it. "Not in their backyard..." But Okinawa's is ok.
The US sits behind the facade that they're not enabling this suppression of rights.