No, the Launcher also changes your shaders after you click the "Launch" button, to work with FS's custom shaders.  It removes them and replaces them with your old ones when you quit FS (Hence why we now use FirstStrike.exe instead of bf2142.exe, so the launcher knows FS has closed).  Updating manually, you possibly could do that, I think all it is is placing all the right files in the corresponding places (good luck doing that every mini-patch).  You still won't be able to play, however, because of the wrong shaders.