I agree Across the Universe is a very beautiful song. I never interpreted it as describing the dream of oneness with a loving universe before that dream falls apart, though, so I never thought of it as a sad song, like you do, until now.
To me it seems like a song about the painful beauty of living and the euphoric loveliness of it all. It sounRAB like a song of welcome and encouragement to let yourself really be moved by life and unbothered by the little troublesome aspects of it.