A combat round consists of both sides firing at each other. A battle is made up of one or more combat rounds. The sub firing and then the cruiser firing back is one round. Assuming both survive that round, the sub, being the attacker, then has the option of fighting another round or retreating.
Normally, fire in a round is effectively simultaneous. The attacker actually rolls first, and the defender chooses casualties. However, when the defender then returns fire, even the units that were hit get to fire, as all units are considered to fire at the same time. The sub Surprise Strike ability simply allow subs to fire first, before anything else. This means that if they sink their target it doesn’t get to fire back. The rule you referenced indicates that a sub that gets a Surprise Strike (fires first) doesn’t get to fire again in the same round when everything else fires. In the next round, it’s free to fire again.
In your example, the sub fires first, its casualty (if any) is removed, then everything else that survives gets to fire. In this case, “everything else” is just the defending cruiser. After the cruiser fires, the round is over, and the attacker chooses whether or not to continue the battle with another combat round.
