The presence of the Orion's fightercraft group in practice cancels out the deficit of antifighter armament. The same really can't be said of the Hecate's lack of anticapital weapons.
On the subject of what can and can't be retrofitted to a ship, the basic rule of thumb is that you can fit whatever guns you want, since they're on the outside of the ship and easy to add or remove, so long as you can also supply them with power/ordnance. In the case of Avengers (or flak guns) this means magazines, ammunition feeds, and major internal restructuring. Such a refit would take a month or more of time and major resources, but would be doable.
On a related note, it probably isn't unreasonable to assume that the Orion didn't originally have facilities to handle the Harbinger as regular fightercraft ordnance, and so they couldn't be kept in the magazines, but rather on the hanger deck. In the open. Where a multiton fighter might bump into them. Can't have been good for the morale of the crew, and it would have slowed down flight ops. (Which might explain why the Bastion was so slow to get off the entire strike at the Lucifer.)
