Consider a specific case: if a 'wrong' was 'damage to a ship' on the starboard side - causing said ship to list - and another, intentional but measured/controlled 'wrong' was judiciously affected to the port side such that the list was corrected, the ship 'righted', lives saved, etc. - it would be true that 'two wrongs make aright' (the ship in this case).
Is this a retort? Not yet, but it does provide a basis for defense of the initial 'proverb' (which it is not, biblically speaking).
Like many sayings, intended meaning is dependent on the meaning as understood by the speaker (even if colloquial / common), perceived meaning as perceived by a hearer. Only after establishing 'intended meaning' can useful dialog begin.