On most Linux distributions, Firefox is built from source and then shipped via a package manager. At least on Arch, --disable-eme is not passed as a configure flag. Yes, one could build Firefox oneself, but it is a beast to compile. It is also ridiculous that this needs to be done at build time.

A perhaps easier approach that should work based on the name (but have not confirmed) is to lock via the user.js method user_pref/lockPref("media.eme.enabled", false). If this works as intended, then simply make this config file part of the deployment should be enough.