I disagree. I think Portal is on the same level as a great work of literature. As an aspiring game developer myself, I feel one could analyze Portal as "the perfect game" in exactly the same sense that a classic may be described as "the perfect novel". That's not to say it's the greatest or cannot be topped, but that it took an idea, explored it to its ultimate depths, combined it with supporting elements, and finished up strongly. That there is a Portal 2 in development is immaterial: Portal 1 stands on its own as a self contained work, and in that sense I think it is very much like a great novel.
Unlike a great novel, automatic updates have changed the ending sequence to better lead into the sequel- a trend that we will likely see more frequently in the future. Does that interfere with a work being "perfect"?
I don't think it does. Just because it's perfect doesn't mean it can't be made better, or that it can't be modified to better suitit's enviroment.
The gameplay, dialog and story that made it so fantastic remain, and the modifciation, if anything, shows how powerful and different it's medium is. Being able to modify a work after it's been delivered is a very new concept, but I don't see how it harms the work. Of course, we do have the special editions of Star Wars, that many people see as a negative thing, but I think new ways for the creator to interact with his work are a good thing.