I would argue that adding "Hurogok Repair Team" as a standard Covie upgrade for most ships would be flavorful and logical; not every ship had Engineers, but the ones that did massively benefited from them. This ability would give Covies an increased hull/shield/both regen rate, which would of course be extremely useful (as someone else in the thread stated) for surviving the UNSC MAC onslaughts. It could either be a passive all-around heal, OR an activated ability that only works for a few seconds; whatever makes the most sense. Maybe you could even have it be a toggle ability, where having it on increases hull/shield regen (at the cost of weapon power as the Hurogoks tap into the energy for the weapons to do what they need to do). A couple of things could be done there.
Give planetary bombarding ships, like the CAS, an ability based off the Luminary from Contact Harvest. If you don't remember, it was a piece of tech designed to locate and map Forerunner artifacts. When the Covenant first located humanity on Harvest the Luminary on the Brute ship in question lit up like a Christmas tree all around the planet with the glyph for "Reclamation", leading the Covenant to assume that the planet was covered in holy artifacts. But in fact, (this is sorta spoilery if you haven't read it) the glyph was not Reclamation, but Reclaimer. The Luminary was picking up every single human colonist on the planet. All ships have a Luminary. However, it seems that by 2550 there was a delay in the installation of Luminaries in vessels (and, so you know, Truth put out an order that one in every 64 Unggoy would be killed every day until a ship had it's Luminary installed.) The ability would basically assume that none of the ships had a Luminary installed until the ability is purchased. At that point, the ship master of that vessel would now have a perfect map of the major human cities and colonies on a planet, and they would know to target that location during planetary siege. Thus, it would be much faster/the ship would do much more damage against a planet with a "modified" Luminary. The explanation as to why the Covenant didn't question why the Luminary was targeting humans could be as simple as "Oh, well it would appear that the Luminaries are targeting the heretic filth that seeks to destroy our gods' creations. Use it to your advantage and wipe them out." Truth already lied and said that the Luminaries are incorrect (which is heretical, as a "Luminary cannot lie," but then this is Truth and he got away with a lot).