Of course the windows that you see are the eastern windows of the Basilica. Some liturgical historians believe that the whole congregation in the ancient basilica faced East during the canon but I cannot really believe that. Unfortunately nobody actually wrote down what they saw and did in the basilica in the late Roman Empire.
Apart from the Ordines Romani, which concentrated on what the clergy had to do, the only depiction we have of the original Basilica and its liturgical practices is from the Pola casket, a 4th century ivory bas-relief showing the pilgrims making offerings and praying at the shrine. They are shown next to the shrine praying in the orans position facing east (the viewer is facing west).
However, I just noticed the traditional separation of the sexes as I was uploading the images. It is traditional that the men pray on the right hand side of the church and the women on the left hand side (a practice that has died out in the Latin church). So it shows that the basilica was really oriented eastwards with everyone facing the front doors. There may be something about that theory and that in early Christian times they were not bothered about facing the Altar during the Mass (something that we would consider disrespectful).
The problem then is when you get to Santa Maria Maggiore (built mid 5th century) you face North when you face the apse and the Altar, so what they did there I have no idea. I think considerations of real estate took precedence over theology. Mind you the Blessed Virgin Mary surveyed the site of Santa Maria and so the architects just followed directions.