One band stopped outside St Patrick's on Donegall Street and played the tune, despite a Parades Commission determination that only hymns should be played and that the parade should not stop.
A number of other bands are also said to have played sectarian songs near the church, where tensions have previously been heightened over similar issues.
Speaking from Rasharkin about what happened at St Patrick's on Friday morning, Rev Gibson did not feel there was a problem as the church was closed at the time.
I notice the doors were closed on the chapel - it's an empty building. Had it been in service, the bands would have played hymns or whatever.
Rev Mervyn Gibson, Orange Order
"We have adhered to our comprehensive template," the Orange Order chaplain said.
"It's a main commercial street into Belfast. If people go along there, they're going along to be deliberately offended."
Rev Gibson added: "I don't believe it's a deliberate defiance.
"We will protest against the Parades Commission, but we're out to have our traditional Twelfth - to enjoy it, not to offend anyone."
Sinn Féin Culture Minister Carál Ní Chuilín has said that the issue needs to be addressed.
"Bands played provocative and sectarian tunes passing both St Patrick's and Carrick Hill. Indeed, one band actually sang the racist Famine song seconds after passing St Patrick's," Ms Ní Chuilín said.
"Several unionist politicians also took part in the parade and the question they need to answer is - are they condoning the breaking of the law and this blatant sectarian and provocative behaviour?
"This lawbreaking needs to be taken into account by the Parades Commission in future determinations, and the PPS and PSNI need to take action or this flouting of the law will continue."
Head of Friday morning's parade, amid a heavy police presence, around 100 nationalist protestors gathered in the area and waved a flag saying: "Respect St Patrick's Church".
Does the Orange Order who organise these parades support this behaviour?
Culture Minister Carál Ní Chuilín
Frank Dempsey from the Carrick Hill Residents' Association told UTV that local people felt "disappointed, angry and betrayed".
He said: "The determination smashed again ... They have danced the whole way through these determinations and once again we see the police enforcing the determination in the people of Carrick Hill and totally ignoring what is happening here."
The parade has since passed through the area without major incident.
During the main parade, Orange leaders staged a protest at the Parades Commission's headquarters in Bedford Street and attached a banner to trees outside Windsor House.
County Grand Master George Chittick said that the Order "denounced" the watchdog, which it claimed had only arbitrary power.
He added: "As Orangemen at the Battle of the Boyne, our forefathers got rid of arbitrary power and we will not accept it now - never. No surrender."
Police say they are continuing to monitor developments and that where there are possible breaches of the Parades Commission rulings, they will be investigated.
On Friday evening, the return parade also passed off peacefully - although, at one point, a stand-off did develop at Clifton Street as Orangemen and two bands tried to walk back towards the church.