There are at least eighty-nine examples of Classical temples turned into early Christian churches.^(1) One obvious ancient parallel with the Haig Sophia would seem to be the conversion of the Parthenon into a Christian church, some time in the late 5th or early 6th century. Interestingly, this doesn't seem to have caused a great uproar - as far as we can tell, it seems to have passed largely without comment. In fact, we don't even know the exact date.

Athens was a particularly unreceptive place to Christianity - Paul's initial reception in the city was decidedly lukewarm and there don't seem to have been any Christian churches in the city until the fifth century - what worship happened was conducted in private houses, and you can get a general view of the strength of Greek Christianity from the fact that only three bishops from Greece attended the Council of Nicaea in 325, against 200 from the eastern provinces. Indeed, Athens remained, through its Academy, the centre for philosophical education in the Roman world, attracting scholars and students from around the Mediterranean - and as Alison Frantz notes, it was very rare to find Christians involved in that.^(2)

The only contemporary comment I can find on the matter is from Marinus of Neapolis, a Neoplatonist philosopher writing a biography of Proclus the year after the latter's death in 485/6 AD.

[Proclus'] choice of the philosophic life amply proves how dear he was to the goddess friendly to wisdom [Athena], But the goddess testified to that herself when the statue of the goddess which had been erected in the Parthenon had been removed by the [Christian] people who move that which should not be moved...

Both Marinus and Proclus were pagans - this is just one of the many points in the Life that attributes Proclus' wisdom and philosophical greatness to the Hellenic gods. I'm not a philosopher and so will try to tread lightly on the finer points of Neoplatonism, but it can to a large extent be read - certainly by the fifth century - as a recasting of Platonic and other Classical Greek philosophy in a way that responds to Christianity and provided upper-class Pagans with an intellectual and philosophical framework to compete with and oppose the Christian one.^(3) Indeed, the Neoplatonist Academy was the main force acting to resist the Christianisation of Athens throughout Antiquity, until it was forcibly closed in AD 529.

Given that, Marinus' comment is hardly outraged condemnation - he doesn't have Athena promise vengeance upon the Christians, nor does he pass anything but the mildest of negative comments. Athena simply decides to shack up with Proclus and to become his patron.

Indeed, though enforcement varied by time and place, the destruction - sometimes compromised down to conversion - of pagan shrines was imperial policy from AD 435. This process happened across the Roman world and involved some of the most iconic temples in existence - the Pantheon in Rome, for instance, was converted to a Church in 609. Interestingly, the Christianised Pantheon was 'sacked' by the emperor Constans in 663 - the eighth-century Lombard monk Paul the Deacon recorded how outrageous this was, and how Constan's later murder was divine retribution for this and other acts of impiety, but didn't mention any reaction from the people of Rome.