Yes, it's common; yes, EE and other things that share similar characteristics are often considered overpowered; yes, the players throw a fit when you disable them - some of them are nicer and just beg nonstop unless/until you put them back. So no, don't feel like you have to have anything enabled on your server that you don't want enabled on your server. I'd probably turn mass fabs and mining lasers off too, except then your players will never know the joys of quantum armor and drilling 25 blocks deep through solid rock... :)