Found a solution to prevent apps from being enabled/visible.
Simply copy your application apk from /data/app to /sdcard/ then uninstall the app, and then copy the apk from /sdcard/ to system/app/ Finally reboot you device. This will give your app system priviligies.
Now you can use the following code to enable/disable your app (making it completely invisible, even from the settings menu):
PackageManager pm=this.getPackageManager(); pm.setApplicationEnabledSetting("com.gueei.applocker",PackageManager.COMPONENT_ENABLED_STATE_DISABLED,0);
Only thing is you have to know the package name of the app you'd like to show/hide. If you don't copy your apk to /system/app/ you will get a permission denial error.