[Nanaki]

You should have the 'Sixth Sense' perk on your hero by then, activate that and use the time to take down the cruisers before they can seriously harm your mothership.

It is very deliberate design that capital ships are extremely difficult opponents even for a fully kitted out squad. Luckily mandatory capital ship fights are few and far between, so you should be okay using your abilities and missiles on them because you should be able to (in theory) recharge and restock before you fight another one.

Also, I recommend getting the best System Firmware you can get. Capital ships were designed in a way that they pretty much excel as tanks, and nothing else, and System firmware fits in with that. Weapon and flight firmwares are unfortunately useless.