Rebels have no upgrades. They are not fully upgraded Vor'cha's. The fleet spawns are also not that large, the largest has a range of 300-320 points. That should be around ten ships, with an average respawn time of about 15 minutes. As it is a late game technology, they should be relatively harmless. A handful of turrets go a long way, particularly since, as they have no siege capability, they simply run up to any point of fortification to die.
The only way rebels should ever be a big problem is if you don't pay attention to them and end up with multiple spawns going in the same well. As they can't bomb, they will never kill the planet off and continue to build up. This would be a sign that you play bad. They had to be weak enough for the AI to deal with them, that it can is a major indication you should be able to as well, considering the AI defends like crap.
By comparison, the Borg can send more firepower into a well of their choosing for every Unicomplex they upgrade appropriately, and have it be under side control, with all of their research applied to them. If you can't stop the Klingons, you have no hope against the Borg.
This isn't meant to be insulting, you're just doing something horribly wrong is all. A small set of clustered turrets should be more than sufficient to prevent major damage from these incursions. They are significantly larger in the Entrenchment version, spawn more frequently, and a group of twelve can destroy them and repair to full strength before the next wave consecutively hits the same planet.
As the Federation, try putting six turrets around a hangar, do ten and you should never lose a single structure to them again. They're back to full strength between attacks even without repair. In a large empire, six will do it with firepower to spare and only the occasional replacement of casualties.
