You're really trying to soft peddle this. Normal members of the military are free (as much as anyone is free, cause this is a casual universe) to regard anyone they like as an enemy or a friend. They're induced to act in certain ways because the military is good at that, but their thoughts are their own. Social conditioning implies strongly that they aren't. Control can make you believe X is friend or Y is foe basically just because they want too.
That's not the same as some random western civilian who regularly disagrees with the government on a whole host of issues.
We can go around and around as to this, but let me make a different point.
Narratively, your interpretation of Conditioning basically absolves the vast majority of the Technocracy, everyone but Control, of the things it did which were wrong. It's the "I was just following orders" defense. I don't like it anymore than I liked M20 going "well, all the Technocratic and Traditions leadership were Sekrit Nephandi" because it basically absolves everyone who isn't a high-level leader of any wrongdoing. It makes them inculpable, because they never really had a choice. You just need to go in, punch out some old wizards and scientists, and then you can create the new, better, Technocracy and Traditions, with all the former good parts and none of the bad. Like, under your interpretation, every Technocrat is legally insane. They could literally commit genocide, and the court would have no choice but to find them not guilty, because they do not know right from wrong. They cannot know right from wrong. It is unsatisfying given how much of Mage's theme relates to personal responsibility.
Why is it that the Technocracy thus gets a 'get out of jail free' card of "I was not literally a member of Control, therefore because Control was actively overriding my sense of right and wrong, I am innocent of everything and have never made any meaningful chose to do bad?" It flies in the face of even the anti-Technocracy bits of the game, because it means the Technocrats you are fighting are not evil, but woefully sick people who need to be pitied. And that's not a good place to be.
Ascension actually points out that Control and Conditioning play this exact role-they exist largely to self-justify, so a Technocrat who does something horrible doesn't have to face it, but just can go 'Control said so, therefore I had to do it/clearly I was right' and avoid having to deal with that problem. And it makes sure to point out that it's a hollow absolution. A Technocrat is still a mage, a god with no masters save those who he chooses to take on.