As a matter of ecclesiology, the parish secretary has no ecclesial authority whatsoever. As a matter of practicality, she has as much lay authority as the pastor entrusts to her. In the human organizational structure of the Church, pastors across the spectrum from parish priests to popes have worked closely with secretaries and depended upon them for day-to-day management of the priest’s non-clerical responsibilities. Take, for example, Pope John Paul II, who depended upon his personal secretary for close to forty years and entrusted him with many “gatekeeper” responsibilities.
What this means for you and for the other parish directors is that you are either going to have to accept this arrangement and work peacefully with the secretary, or respectfully bring your concerns to the pastor. Either course of action is a valid option, but I personally recommend accepting the pastor’s demonstrated preference of working with him through the mediation of his secretary and only approaching him to ask for a different arrangement if the secretary is unable to resolve your concerns or is otherwise behaving in an unsuitable manner toward the rest of the parish staff.