When I run a dedicated server (using server.cfg), my jk2mpconfig.cfg gets rewritten, getting rid of all my bindings. How can I prevent this? I don't want to set jk2mpconfig.cfg as Read-Only, because then I'll be locked into my configuration.

Maybe this will help:
Create a textfile in your GameData\base directory and paste in all your bindings. Then save the file as autoexec.cfg. If the computer adds a ".txt" to autoexec.cfg delete the .txt part. The settings in autoexec.cfg will load automatically when you start a game.

You could also create more than one configfile e.g. one for darkside (dark.cfg) and one for lightside (light.cfg). To load this settings activate the console in game and type in /exec dark.cfg.

When you're in the game with all your settings set the way you want them to be, bring down the console and type

write xxxxxx.cfg

where xxxxxx is the name of the file (try autoexec since it is loaded automatically)

If you make any changes to your config (video, controls, whatever) make sure to do the above again.