How about reducing player frustration while keeping the guardians dangerous (as they should be, otherwise the game would get boring)?
1. Spread the damage.
1.1 By letting the guardian switch target areas of the ship
1.2 By letting the ship automatically spread damage from heavily damaged ship parts to less damaged ones.

(to 1.1 and 1.2: Perhaps only after a certain damage threshold for a single part is reached.)

1. Make the guardians priorize drones above the ship. 2.1 As long as the guardian sees a drone it will attack it. 2.2 As long as the guardian itself is attacked it will attack a drone, not a ship, possibly and logically one of its attackers.

To 1: The side-effect is that a ship with lots of components will be able to withstand enemy fire longer. This does not replace armor, because the sum of damage dealt will still be the same, as will be the repair costs. Guardians will not be able to burn a hole into your ship within 30 seconds as is now often the case - in my experience at least, and my build is clearly suboptimal.

To 2: This will effectively reduce the danger to your ship to 0 AS LONG as you actively engage all threatening guardians. Life for the drones will get a bit more dangerous, though. And if you ignore a source of danger they will burn a hole in your ship just like before.

I guess suggestions 2.1 and 2.2 (mutually exclusive, unlike 1.1 and 1.2) would be much easier to implement, since they probably just require to update the targetting algorithm.