Native speaker here.
Führer and Leiter seem similar in meaning, but are really quite distinct, both in denotation and connotation. And, contrary to what grandparent poster said, Führer is by no means dead.
"Führer" means guide. As in, a mountain guide ("Bergführer"), tourist guide ("Reiseführer" - both guide book and person), or driver of a vehicle: driving license ("Führerschein").
Similarly, "Anführer" is a leader of a like-minded group, often in the sense that he is not a formal leader. To pick an example from current affairs: Carles Puigdemont is (formally) the president of Catalunya, and (informally) the leader ("Anführer") of the independence movement. There is quite a number of words derived from Führer.
The verb "leiten" means to direct. Thus, a "Leiter" is somebody who gives directions: a director. This was, and is, a reasonable word, especially in a professional context.
To explain the Nazi diction a bit. Think of uses like Bergführer ("mountain guide"): somebody who leads his charges skillfully through treacherous terrain. I suppose that was the kind of image the Nazis wanted to project on Adolf Hitler (who you are of course referring to). It's true that Führer may sound politically piquant to German ears, but only in quite specific contexts. It's a pretty normal word.