If he was truly a general then why at the Imperial camp near Doma does the soldier make a comment to the effect of "if Kefka becomes the next General I am leaving." That makes me think that he is there as an observer from the emperor's inner circle, but not truly in the capacity of a General. Now maybe later on after Celes joins the Returner's and Gestahl realizes Leo will never aid him in fulfilling his goals maybe he makes Kefka a General, but I don't think so. I believe Kefka is simply a high(well highest) advisor to Gestahl and most trusted of all Gestahl's people.