I assume that your tests run with normal web content privileges. In that case, they aren't going to be able to affect browser settings such as whether JavaScript is enabled (I assume that's what you mean by "toggle JavaScript support").
I'd implement a simple XPCOM component with a method to turn JS support on and off (by setting the appropriate pref). You can expose it as a JavaScript global property so that your tests can access it. See Expose an XPCOM component to javascript in a web page for more details. Package your component in an extension and make sure it is installed in the Firefox instance where your tests are running.
If you want to access the preferences API directly from your content script, you can add the following prefs to Firefox, either in about:config or by adding the following lines to prefs.js in your profile directory:
user_pref("capability.principal.codebase.p1.granted", "UniversalXPConnect UniversalBrowserRead UniversalBrowserWrite UniversalPreferencesRead UniversalPreferencesWrite UniversalFileRead");
user_pref("capability.principal.codebase.p1.id", "http://www.example.com");
user_pref("capability.principal.codebase.p1.subjectName", "");`
user_pref("signed.applets.codebase_principal_support", true);
Replace www.example.com with the domain that you want to grant the privileges to. Also add this line to your JS code before you call the preferences API:
netscape.security.PrivilegeManager.enablePrivilege('UniversalXPConnect');