Now, Spock also manipulates the Romulan Commander very successfully and in some sense, it does play as cruel. But lest we forget, she is also manipulating him simultaneously, using what she perceives to be Spock's sense of racial superiority to harness resentment against Kirk and loyalty towards her. So they are both pawns of the mission. But I would suggest that -- all along -- Spock may have a better future in mind. He may be stealing a cloaking device and deceiving a beautiful woman in the present, but he also realizes that military secrets are fleeting and that one person can change the world; can alter the direction of the future (also a message of another Star Trek episode, "Mirror, Mirror.")
In Star Trek history, "The Enterprise Incident" may actually be one of the most significant episodes of all, especially in terms of impact on the franchise.
Also, although Fontana introduced Vulcan "finger-touching" as a gesture of affection in "Journey to Babel," here we see a more...erotic...application. That too returned to Star Trek, in 1984's Star Trek III: The Search for Spock. Additionally, in "The Enterprise Incident," the audience gets some significant knowledge of the Romulans, from the "Right of Statement" to the command structure inside the Empire.
And furthermore, the Romulans had not even used this cloaking device in battle yet. They had used a similar weapon in the past, on Federation border outposts ("Balance of Terror"), but still, this seems to qualify as a pre-emptive strike, right? Does Starfleet subscribe to the...Bush Doctrine?
In closing, I submit that "The Enterprise Incident" is a worthwhile and memorable installment of Star Trek because in that last scene, Spock acknowledges something important and true. Kirk, the Romulan Commander, and Starfleet itself are all playing one dangerous move in a much larger chess-game. They are focused on that move: getting the Cloaking Device (or getting the Enterprise, contrarily). But Spock is thinking a long-term strategy, thinking several moves ahead, to something more permanent than a fleeting military secret. He was touched by his encounter with the Romulan Commander, more than he ever could have imagined.
On the other hand, you could also argue that Spock's entanglement with the Romulans, begun in earnest in this episode of the classic series, is the very thing that destroys his timeline some hundred years down the road. As the Vulcan himself might note, "fascinating..."