Yeah it's as though when an alien is under your control, the game treats it like its just another member of your team for those three turns.
I think the panicking soldier had spent all his downtime hanging out in the research lab and watching the captured Alien Entertainment units. After a while his social isolation and obsessive fixation on novel forms of foreign pop culture combined to convince him that he was born on the wrong planet and only the Cydonians could truly understand him. Secretly he began to concoct plans to travel to Mars and make pilgrimage to the land that was his birthright, but which had thus far been denied to him by the whims of fate which had thus far seen fit to confine him to terra firma. He began to feel guilty for the way in which he earned his daily bread, and resolved that he would abstain from any violence against his alien brethren-to-be, instead gnawing away slowly at the XCOM project from within by collecting his monthly salary. It was but a trifling resistance, but it was all he could muster.
Then suddenly all his planning fell by the wayside when a series of unfortunate injuries left XCOM in need of second-string soldiers to fill out the numbers of the strike team. A plasma rifle was shoved into his hands and he was sent into combat against the only beings in the universe who could understand him. He planned to keep his head down and avoid doing any direct fighting, but then, in a fateful moment, one of his fellow soldiers seized control of an alien's mind and, heedless of the beautiful culture which it had represented, sent it to its grisly end.
It was more than he could bear. Seeing red, he turned on the nearest XCOM authority figure and unleashed what fury he could muster. The shots scorched the Colonel's armor but failed to cause any meaningful harm. Immediately understanding the folly of his betrayal, he turned and ran into the Muton swarm, expecting them to welcome him with open arms as a comrade they had never expected but who, in retrospect, they had e'er yearned for.
His welcoming party wasn't quite what he expected, but at least XCOM had one less traitor in their midst.
or maybe the game just thinks mind controlled units are xcom operatives idk i think both theories are pretty sound