You're right, those soldiers are very different from what you'd find on a USMC base. But you're not considering that even had that base been outfitted with American Marines, the result would have been much the same. Sure that commander wouldn't have hastily retreated to the rear of the ranks of his men like he did, and those soldiers would've maintained discipline and dignity. In the end though, looking over that horde of well motivated men and women stretching all the way out to the very horizon itself, even the most arrogant of USMC colonels would have realized that this isn't a battle that he's in a position to win. If he ordered his men to fire on the rebelling citizens, it would be a bluff and a gamble: They have neither the manpower nor ammunition to maintain a foothold and would be relying entirely on the crowd fleeing. But the odds weren't in favor of that. There were too many, packed too tightly - many of them would have nowhere to go but forward - toward the soldiers.

What's more: Many of them would call that bluff, and would rush forward to attack. Aside from that, a massacre would create martyrs and would guarantee the situation became far worse very quickly. And that's not to mention that many soldiers would hesitate if fire at all, unwilling to slaughter their countrymen - their brothers and sisters. Particularly considering they too realize that saying they're outnumbered is quite the understatement, and the probability of them surviving such a conflict may be very low. Everyone experiences fear and intimidation.

Be it a Mexican or an American base, it wasn't only going to fall into enemy hands no matter what - it already had.

And no, not every military installation has non lethal weapons, and even had they used said weapons it would be much the same gamble. You don't engage any "enemy" under such circumstances.