http://solidlystated.com/software/minecraft-remove-clouds/ id suggest just google, how to remove clouds from minecraft this does it for you only i believe not sure exactly about your entire server. but this is a good as i can get it
You can either erase the clouds.png in the jar file, or use Optimine+Optifog. With that installed, you can change the height of the clouds, or simply turn them off at will.
You can't force it on your entire server. It is simply a texture pack. It could be possible with BukkitContrib though
