If Megaships can be attacked by a squadron of players and defended by another squadron surely this should be open only content or you will have players killing off other factions Megaships in the privacy of their own server where the owning faction can do nothing about it?
Not sure if i responded to this thread already, so assuming i haven't, just consider this:
Does your player group have people online 24/7 and are those people willing to sit at your megaship 24/7?
Do you think any player group really has this capability? Maybe, just maybe, the largest could, but would they want to sit around waiting for the off chance that someone will launch an attack, and any such attack would likely be in force, resulting in the 1 or 2 defenders getting totally stomped.
Based on that, what do you think the chances are that FD will make the carriers destroyable in any way? Perhaps raidable for components, that reset, just like a megaship. But no real loss. So you can defend if you want to, and are online, and in the region, etc.
In short, its highly unlikely the carriers will need to be defended from attackers, and most likely will behave more like stations.
In which case, your question/point is pretty moot. There is no need for it to be open only.