I understood the ending in a completely different manner.
See, the last Blue was the ultimate Blue and was protecting the very essential core of the Blue infiltration "therapy" - and the one Blue did indeed die! Once Yuji entered the glow, and the beam itself - he could see all the history of the Blue from Earth's perspective so that he would understand! The beams emanating from different points symbolised for me the Blue leaving the Earth once for all (or for THIS time).
In fact, according to various sources, including Wikipedia, the Blue were the Earth's immunisation method to get rid of mankind which had become something like a cancer to Earth, destroying it slowly. So, Earth wanted to destroy all the "old" generation of people.
http://en.wikipedia.org/wiki/Blue_(Blue_Gender)
I didn't feel when the people went berserk on 2nd Earth that it'd be connected with the moment of eradication of the Blue ... but as you point out - it could be it also.