That's it. You don't need to delete your files first. All it will do is fix your gameinfo.txt and copy over the MM:S .dll -- a single file. You only have to do this once, and it will be good for all time.
Ok, so I tried this to one of our servers the other day.
Then tonight's update rolls out. The server that uses metamod.vdf has the usual issue of the file deletion and MM & SM disabled. The other server, where I used the autoinstaller, and deleted metamod.vdf manually, just hung offline until I restarted it.
So 2 broken servers with different issues.