iiiiif i'm not mistaken, i've seen somebody who have tried to delete std facebook app via terminal on russian forums. The removed app pulled some dependencies with it, but unfortunately these dependencies where necessary for other apps, so after that the N9 had to be reflashed. If I'm not mistaken.
That's why it's better to remove the .desktop file, not the whole program, until you don't want to mess with all this mumbo-jumbo in the sake of some 10-100 megabytes.