Lots of great ideas in this thread.
I'm all for optional, I think it's fun as is but it would be nice to switch it up. +1 to Vladimir and Orosian.
I liked the way it worked in Birth of the Federation. Taking the homeworld wasn't insta-win, but it put them at a huge disadvantage.
As for making the Spell of Unity un-counterable-to do that it would have to become a lot harder to get. Playing on a XL map with the max number of worlds and leaders one of the ai nations started casting it on turn 165 or so. There's no way the "science-type" victory should be reachable in that circumstance. On the flip side, I do agree that being able to just burn 1 turn of casting to stop it is less than desireable.
Nothing wrong with being optional, but I'd like to see it gone.