I'm not sure what Joomla Comment is, in all honesty. If it's a Joomla's comments component, that's not related to Facebook, you can likely leave it on (or disable it) whenever you want. It really depends on how you want to integrate Facebook's comments.. either with a separate commenting extension (so a user can use either) or just using one. If it's another Facebook extension, you'll likely want to disable it sooner than later as other extensions that include the Facebook library can cause conflicts in multiple areas.
Hope this helps, and good luck!
Joomla Comment
