Indeed, there is no dialogue reference to weapons deactivation, and no visual cue that the weapons would fail to fire.
So obviously, the transporter deactivated the Klingon initiative instead!
Presumably for the same reason they couldn't detect the absence of a planet below them when a security detail got beamed down into empty space in "And the Children Shall Lead." And for the same reason the transporter has occasionally beamed aboard energy beings and the like without anyone knowing it at first. Because the script says so.
I'd think it more natural to assume the most common of all technological failures at work here: the user error.
In "Man Trap" and "Children Shall Lead" alike, the transporter operator would quite probably be under the mental influence of the alien villain of the week. The instruments might show something odd, but the operator would simply ignore the disparities.
Granted, we didn't exactly see a child shaking his or her fist at the transporter operator in "Children" when the oopsie happened. But it would make plot sense for the children to "program" the transporter guy the same way they programmed Sulu and Uhura, with lasting effects that do not require the presence of a fist-shaking supervisor. They obviously casually programmed random background redshirts anywhere they went, so that those would not report on the strange rituals the kids performed...
And it doesn't really seem as if transporter operators
ever scrutinized the sensor readings before proceeding with a standard transport. We have little idea how this "three to beam up" thing works, but no operator has ever complained when the landing party leader has ordered an extra number to be beamed up, or has swapped one of his team. It just isn't relevant to check what is being transported, unless one suspects "contamination" in the first place.
I mean, how often does the garrison gate guard
really ask for ID when a person in uniform arrives in the company of a trusted officer? The tedious task of flipping three additional switches and glancinc at a dial might well be left undone in the mundane event of somebody transporting up to the ship.
Timo Saloniemi