Ideas:
Modular Dispersal - The Assault Carrier disconnects breached modules from the vessel, decreasing the damage that has occurred. [Replenishes an amount of HP/ Will have a long cooldown]
Covenant Invasion Force - The CAS deploys a large Covenant attack force planetside, increasing the time taken to conquer a planet. [A planetary siege ability]
Tactical Scarab - When all else fails, the Scarab is dropped to clear up, increasing the time taken to conquer a planet. [A planetary siege ability]
Divine Influence - The presence of a Prophet directing the fleet inspires all as they commit themselves to the will of the gods. [increases the capabilities of all ship systems. Speed, damage, shield and antimatter recharging are all increased for a time]
Wrathful Fanaticism - The holy sermons of the Prophets are played endlessly throughout the vessel, throwing the crew into a fit of zealous rage. [Increases the weapon damage of the CAS for a time]
Overcharged Excavation Beam - The siege is dragging on longer than the Fleetmaster had predicted, cleansing beam to full power, purge the filth. [A planetary siege ability increasing the cleansing beam damage for a time]
Anti-Matter Boarding Party - Only the most faithful of Spec Ops take on this mission, boarding an enemy vessel and detonating an Anti-Matter bomb at its black heart. [Essentially the same idea as presented above]
Hope it helps!