I don't know anything about the setting you want to model in this OOB, but the "swarm" organization you describe made me think of something that was discussed to figure radar-centralized SAM batteries.
If you want a pack of units centralized around an all-powerful leader, create a large platoon-level formation with eleven "squads" led by one specific unit as you described.
The squads should have maximum manpower, a negative morale modifier and
no radio. In this case, they will have to stick around the leading unit to gain command access, and there are great chances that they will rout once the leader is destroyed.
Also, don't forget to put the leading unit in a different unit class, so an IA pick will not mix both types.
About anti-air weapons: are these vehicle-based or not? If yes, you could use a class 4 weapon (AA gun/MG) with a weapon size of 4 or more. These will be the most efficient against both air and ground targets, but IIRC the weapon size will drain more ROF and leave less firing chances per turn. Add a deliriously high accuracy rating and a large positive unit experience modifier, and you should have a deadly enough weapon.
Also, fiddle with the warhead size and HE kill ratings to adjust the damage and animation to your liking.
Lastly, if you want this weapon to be efficient against armour, my take would be to give it a large HE penetration, thus sparing superfluous AP shots. This method tends to work too well for real-life weapons (makes them too efficient against armour), but since we're talking plasma guns...
And if it's an AA-oriented weapon, the large ROF burst fires could even account for the occasional collateral plastering you would get against multiple armored units stacked in the same hex!
