By the 5th century, it coulda been the Christians doing the torturing, for all we know.
Or it could've been simply a 5th century crime, and maybe that desecration is what led to the cathedral's disuse.
Before the Muslim onslaught people forget that the Zoroastrian Persian/Parthian empire over ran and destroyed many of the Greco-Roman cities before the emperor Heraclius defeated them in what some historians called the world's first Crusade. The Zoroastrians had taken the relic of the True Cross as a war trophy when they looted Jerusalem and destroyed the church that was atop the temple mount.
The Muslims took advantage of this weakness from the war the Romans and Parthians fought to first take over the defeated Persians and then take the Middle East from the weakened Romans.