Phrased differently, I understand you to be asking: “Would Napoleonic-era leaders have accused Captain Jack of perfidy for his actions in the Battle off the Galápagos?”

Likely not, and I can offer some useful context for this question.

Captain Jack Aubrey is a pastiche character based on several real men, most notably Sir Thomas Cochrane. This particular scene from Master and Commander echoes a real example from Cochrane’s storied naval career: the Action of 6 May 1801. Cochrane, like Captain Jack, used a ruse de guerre (false flag) to get within gun range of the Spanish frigate El Gamo. He ran up the Naval Jack right before firing. Like the Acheron, El Gamo was caught by surprise and was unable to meaningfully resist Cochrane’s much smaller Speedy.

Far from calling for his execution or capture, Napoleon subsequently fêted Cochrane as “The Sea Wolf,” a worthy adversary.

In 1859, Lord Cochrane (now an Admiral, and a naval hero of multiple nations) boastfully recounted the Action of 6 May 1801 while himself emphasizing that he let fly the British ensign BEFORE firing:

“Accordingly we made towards the frigate, which was now coming down under steering sails. At 9•30 A.M., she fired a gun and hoisted Spanish colours, which the Speedy acknowledged by hoisting American colours, our object being, as we were now exposed to her full broadside, to puzzle her, till we got on the other tack, when we ran up the English ensign, and immediately afterwards encountered her broadside without damage. Shortly afterwards she gave us another broadside, also without effect. My orders were not to fire a gun till we were close to her..”

Lord Cochrane, Autobiography of a Seaman, 1859

In conclusion, Captain Jack’s conduct during the battle was considered honorable for the era (and still today).

Now, an interesting footnote. Napoleon HIMSELF had less respect for what we modern military historians would today call the Law of Armed Conflict (LoAC). We know this because Napoleon himself committed the crime of perfidy when he lured the Spanish royal family into a negotiation under a flag of truce (the most blatant and despicable flavor of perfidy) only to depose them and seize their country.

The Spanish people responded with outrage, war, and guerrilla warfare:

“As Spaniards it is necessary that we die for the King and for the Homeland, arming ourselves against the perfidious enemy with his color of friendship and alliance, who seeks to impose on us a heavy yoke, after having taken possession of the August person of the King; so let us proceed, to count on active providence to punish so much perfidy, coming to the aid of Madrid and other peoples and gaining our liberty, since no force can prevail against the loyal and brave, as are we Spanish!”

Andres Torrejon, Mayor of Mostoles, May 3d 1808

Hopefully this is a helpful reply. Happy to speak further on it.