Perhaps the question can be answered in two ways:
Ideally, was it canonically supported? No
Did it happen? Yes
I would refer to the initial question, is apostasy punishable by death?
The answer is no, it has never been punishable by any kind of bodily harm, and we have no reference that it ever occured as a violation of those canons and the faith itself.
The same we could say for heresy - being the gravest sin along with apostasy - it has never been punishable by any kind of bodily harm, yet:
1) It did happen in 6th century towards the clergy and faithful of Church of Alexandria, known these days as Copts. Though it was primarily conducted by the state/government, as enforcement of the laws of the Empire, there is no doubt that Constantinoplean Patriarchate did participate in it in violation of the faith and canon.
I'd note that differences that were behind it occured at Chalcedon (4th Ecumenical council) in 451, but the persecution happened after 5th council (Constantinopolis, 553) after an unsuccesfull attempt of a union. That should be born in mind by present-day-ecumenicals.
The fact that at present days, though pre-Chalcedonians do reject the 4th Council, the disputed issue about the mode/fashion of union of God and man in the person of Christ is regarded a bit different that it was now. It is now clear that there would have been better understanding if there were no new terms/words involved - phisis, hypostasis and ousia
, and if all of them had the same understanding of words - not to mention Copts (and Armenians) do have their own language and don't communicate in Greek.
Therefore, I believe I've heard the statements both from Copts and Armenians that they never professed what's been condemned in Chalcedon as heresy, and I never read an Orthodox who was willing and able to prove such a statement false.
2) It did also happen in case of St. Maximos the Confessor whom was persecuted by iconoclasts for his Orthodox stance towards icons. He is Saint now.
3) It did happen in case of Avvakum, whom, I believe, is a Saint of Russian Old Believers. A branch of Old Believers entered into communion with ROCOR and, when ROCOR restored communion with MP last year, that also marked restoration of communion with one branch of Old Believers.
It should be noted that dispute with Old Believers was about how many times Alleluia should be sung - two or three times - at certain parts of liturgy. Russian Tzar Peter the Great wanted to correct some errors occured during translation of liturgical practices from Greek into Russian. I've read a statement of MP (or was that an interveiw of a bishop?), saying the "correction" also contained errors - so in that case replacing one error with another at the request of a reforming Tzar inflicted another wound.
So, Ireneos, there you have three cases in history where, in violation of Faith and Canons, punishments did occur. If that make it easier, victims are Saints now, at least to some Christians, and it happens to be that common opinion is that none of them did profess anything contrary to Orthodox Faith.
So, go figure.