In my opinion 9/11 wouldn't have happened. If you read the history of that war/invasion, we secretly funded the Taliban to fight the communist part. It would be there Iraq, I support our troops but no invasion or war can go on for 10+ years. I think that you would have had several terrorist attacks in mainland Russia.
In my opinion, if the Soviet Union had annexed Afghanistan it could have sparked greater resistance on the part of the Afghans. The Soviet invasion was sparked by the weakening of a Pro-Soviet Communist Government in Afghanistan. Visit http://en.wikipedia.org/wiki/Soviet_Union for additional details.