I'm not sure what your point is supposed to be. They shot something early on that wound up getting edited out of the film because they found that it didn't work as they edited the film together. That's how these things are made, and more directors should learn how to exercise such judgment (*COUGH*PETERJACKSON*COUGH*).
Yep. I don't see any indication that they went into production without a finished script; Singer just said that, as they were editing, the scene in question was discovered to be not necessary and a good place to trim the fat. I've read interviews with writers and directors where they say the editing room is often seen as where they can have a last "draft" of the script, because they can finally see the movie as a whole and see what works and doesn't.
As an extreme example of how this happens, Billy Bob Thornton, Martin Sheen, Jason Patric, Gary Oldman, Bill Pullman, Lukas Haas, Viggo Mortensen, and Mickey Rourke were all completely cut, and Adrien Brody's role was changed from being the protagonist to having only a few minutes of screentime, from The Thin Red Line during that film's editing process.