This is a very good question (and, by the way, congratulations on your English). You have put your finger on one of the mysteries of God's action, namely the fact that he works through human instruments.

Regarding obedience, the Church teaches us that we obey God by obeying our superiors. You obey God in the superiors because what they ask of you is what God wants you to do. Of course there are things that a superior cannot ask you to do  ("Here, take this poison and drink it" or "Teach your students that the Pope is not infallible", for example) and if he does you should not obey him. But these are the rare cases. Usually our difficulties arise on practical matters, when we may see things differently than our superiors. Most often superiors will accept input because they dont want to make mistakes either, but sometimes they have information they cannot divulge that influences their decision, and so we have to obey at times without understanding fully.

The example you brought up about the Inquisition is not a good one because there is so much misinformation about the Inquisition in our popular culture and even in our history books. (Did you know that the accused people often preferred to be judged by the Inquisition rather than the Emperor's courts, because the Inquisition was often more just and flexible?) I hope this helps you; there is a lot more to be said, but I think the above touches on the essence.

God bless,