The settings are global in presence.js or individually set for each user. Individual user settings are context aware. look at the fop2settings.db with sqlite3 to get an idea.

Then add the preferences permission to the user you want to modify, open up the preference from the browser and turn off sounds. Then you can remove the preferences permission, but the sound will remain turned off.

Log into fop2, you have a preference icon at the top right if you have the "preferences" permission assigned to the user. You can set several preferences there, including turning sounds off.

You can edit

/var/www/html/fop2/presence.js

and turn off sounds and set other global parameters, like disabling warning on close, defining the number of line appeareances, etc.

Since FOP 2.30, settings can be configured via FOP2 Manager (http://your.server/fop2/admin). That for global options. Or open up preferences when logged into FOP2 for each user and you can turn on/off all sound types (ring, queue, chat).