Hi

In short YES, if you want the whole world to download your .fla then leave it
on the server.

Flash comes with a handy but not very friendly way of publishiing your site,
ie Publish Settings
What this does is create an html wrapper for your .SWF, which by the way is
created whenever you run your movie inside the Flash IDE. Upload your .swf and
html renamed to index.html if this is your default homepage to your server.

Remove the .fla from the server - Problem Solved.