Well, it's interesting, but the guitar solo is definitly not George's best work. He probably didn't like it enough to leave it in the final version.
Look at Let It Be. George made three different guitar solos on each versions of the song, the video, single and album version.
Also, in Abbey Road, George brought the Moog synthesizer for the band. I think he wanted to put more emphasis on that instrument in "Here Comes The Sun" since it was new for him. This could be a reason why he scraped it from the song. He wanted a new sound, something different.