Explain the reason of separate seating by the Coptic Church of men and women in the Sanctuary. Is this a "church" tradition, or is there a theological distinction being made here?

You asked a question that is frequently asked regarding the distinguished and separate seating of men and women in the Coptic Orthodox Church. Did you know that the separation of sexes in the Church was a universal Christian custom until the Protestant Reformation? This often escapes modern memory. The custom survived among many Protestants until the last century in fact. The early church and early church fathers viewed separation of sexes in religion particularly as an "appreciation of the natural order." It was viewed as a positive occurrence rather than a negative one. Everything had its proper place, according to its nature.

In the Apostolic Constitutions, we are told that the Christian faithful are segregated in church not only by sex but many other things as well. These things included age (women, young women with infants, children, and so on) and vocation (monks, virgins, widows, etc).

St. Cyril of Jerusalem points out, the animals entering the Ark, do so with their own kind:
For though the ark was one, and the door was shut, yet had things been suitably arranged. If the church is shut, and you are all inside, yet let there be separation, men with men, women with women: lest the pretext of salvation become an occasion of destruction. The separation of the sexes in early Christian writings was also seen as prevention of temptation.

The early Church Fathers did not consider the careless, casual mixing of the sexes to be spiritually healthy. Further, as early Christianity attests, did you know that there were wooden partitions separating the sexes in the church? St. John Chrysostom states:
It were meet indeed that ye had within you the wall to part you from the women; but since ye are not so minded, our Fathers thought it necessary by these boards to wall you off; since I hear from the elder ones, that of old there were not so much as these partitions; "For in Christ Jesus there is neither male nor female." And in the Apostles' time also men and women were together, because the men were men, and the women, women. But it is now altogether the contrary; the women have urged themselves into the manners of courtesans, but the men are in no better state than frantic horses.

St. Hippolytus and the Apostolic Constitutions both specify that the "kiss of peace" is not to be exchanged between men and women.

In his Apostolic Traditions, written before 230, St Hippolytus delivered the following instructions for catechumens: And let the women stand praying by themselves in another part of the church, whether they be faithful women or women catechumens. But after they finish praying, let them not give the kiss of peace, for their kiss is not yet holy. Let the faithful indeed greet each other, the men with the men and the women with the women; but let the men not greet the women.

As you can plainly see the distinguished custom of separate seating dates back to the early church and has been faithfully practiced by the Coptic Orthodox Church since its conception.
May God bless you and continue to encourage your search for knowledge regarding Church Worship and Early Christian Teaching on the Man and the Woman.

This Q&A was found on Archangel Michael & St Bishoy Coptic Orthodox Church : http://www.stbishoy.org.au/modules/smartfaq/faq.php?faqid=49