I loveee this idea in bold.. I can't see Kakashi being killed again, but with your idea, it could work at the near end of the series.. Kakashi surely have became OP now, it'll be sick to see Prime Kakashi vs. Healthy Orochimaru with their students (Naruto & Sasuke) battling elsewhere.
I agree that the final opponent for the series should be Orochimaru.. He's one of the Sannin, he has been around since Part 1.. Madara came from 1st Hokage's time, so I'd like him to be sealed away and go back to the time where he belongs. There would be more impact to the plot since Sasuke and Naruto have had many ties to Orochimaru.