They read your mind because they know it won't lie to them.
They should know I was lying when talking to Tchortists then.
Not even the game knows that, as things stand! How could the commander know? Besides, we don't know how the mindreader works. Maybe he just sees the scene of you accepting the quest, divorced of its context, and jumps to conclusion. Maybe he can only view your memories as a movie, without understanding your feelings and motivations.
And they really are not that ruthless, else they wouldn't waste their precious resources o keeping Lora alive.
I've never been able to find out why they kept Lora alive, but based on what I've seen so far, they are ruthless murderers, and not even one good deed changes that.
And even if that was the case, there should be a [lie] option when accepting the reconnaissance quest.
Alright, that's a possibility, but then you should also be forbidden from
actually completing the quest, since your in-game character does not intend to help them. After all, otherwise you are just gaming the system, aren't you?