lots of 3rd party (or commercial) hosters automatically run an update either from their local server images or straight from valve each time the server restarts.
If you are using a 3rd party, your only option is to ask them to change their system - or try and block their update by setting the file to "read only" - but that method could prevent you from getting any future updates.
The way i do it is to copy the gameinfo.txt (along with a few other files that get overwritten) at the end of my update script... That way each time i update a server the changed/updated files get written back into the mod.