I wasn’t exaggerating when I expressed things as I did in class.
The tradition, at least the monastic tradition, is uncompromisingly clear on this point: obedience is crucial, even in situations where it might seem as though one’s spiritual father is wrong, and indeed sometimes even in cases where he is wrong. St John of the Ladder goes so far as to say that a monk should not criticize or abandon his abbot even if he catches him in the act of fornication, though—and this is clearly important—the monk can leave if the abbot teaches heresy. This last qualification shows that the conscience of the disciple is still in play. So yes, you were right in supposing that one’s conscience is never to be “suppressed or denied”.
At the same time, however, it’s important for the disciple to realize that his master may sometimes do and say, and even command, things that run against the grain of “normal” behavior. Needless to say, no genuine spiritual father is going to flout convention simply in order to scandalize people. There will always be a “method to [his] madness”. And I think we might add that a genuine master will always go slowly with a novice, not imposing too much on him too soon. We see a simple example of this in The Way of a Pilgrim in the gradually increasing number of repetitions of the Jesus Prayer the pilgrim is instructed to say. But regardless of the “speed” at which one is brought along the Path, the role of the disciple is to obey his teacher implicitly.
In this sense, I think one could truthfully say (I’m quoting you here) that “free will must be sacrificed”, though only with the understanding that until and unless one experiences the grace of apatheia through the discipline of catharsis—and this is why one seeks a guide in the first place—one is not really free anyway. “In His service is perfect freedom” extends, in the Orthodox spiritual tradition, to the disciple’s obedient service to his master.