Bingo! You have identified the key problem with this show. This is why the Taliban "loses" in this episode--because of the nature of the battle. The same thing is true of the Green Beret vs. Spetznaz and Spartan vs. Ninja episodes. The ninja is forced to fight a Spartan hoplite in an open fight. At the end, one of the ninja team members then said something like: "well the ninja in real life would have run away and then come back later to kill the Spartan in his sleep." And that was my point.
I have never seen or even heard of this show. It sounds interesting, though stupid, for the reasons you mention.
A better match would be Spartan vs. samurai, as the ninja were spies and assassins, not warriors. They fought only when forced to.
A single first rate samurai would probably have taken out a top-notch Spartan in no time. The samurai were individualistic warriors. Spartan equipment and training was not based on individual combat, while that of the samurai was.
For the exact same reason, a thousand Spartans would have demolished a thousand samurai. The Spartans were trained to fight as a unit, and were punished and sometimes even executed for glory-hounding like the samurai routinely indulged in.