In the intervening period, the church went to the Delhi Minority Commission (DMC) and complained that no notice was served to them and that it was done "intentionally". In the complaint to the minority commission, a copy of which is with Swarajya, the church pastor-in-law N C George alleged, "...there are still certain encroached visible structures adjacent to the church which was deliberately ignored. We being minority, feel that the Church has been targeted and was harassed by this illegal act at the time of our festival season." (Passion Week began on Sunday and Good Friday is on 30 March). George is also the president of the Global Council of Indian Christians (GCIC).

DMC member Anastasia Gill visited the site shortly after the complaint on 15 March and concluded that there was discrimination and told as much to a newspaper, "I visited and inspected the site and believe that this is a discriminatory practice. It has disturbed religious sentiments and is an attack on the Christian community. The rights of the minorities are under threat. The area outside the temple next door has not been touched. Is the system working towards maintaining harmony or disturbing it?” She also served a notice to north MCD and the police demanding a reply by 6 April on the allegations made by the church.

It is to be noted that the original complaint by the church to minority commission did not talk about the temple being untouched. However, in statements to the media in the following days, George repeated Gill’s observation and said that they were targeted while a temple was spared.

These allegations were refuted by Rai, who told Swarajya that no notice is needed to be served in these cases as the orders have come from the High Court.

He said, "there were a few structures we encountered before the church that could not be demolished on the same day. Those were built with thick mortar and the bulldozers could not destroy them. I was informed about the issue and had ordered the team to bring JCB machines on the next drive to deal with it and that was done."

"There is no religious angle to this. This is no conspiracy," Rai said.

A visit to the site, conversation with locals and temple authorities, along with photos and videos of the episode, seem to support Rai’s account.

PWD official Jaiswal said that the drive had to halt at some point that day and it so happened that it stopped just before the temple. “All work can’t be completed in a day,” he said, and added that the temple authorities, in fact, had already begun razing down their part of the encroachment (on March 15) as they saw the bulldozers in action.

This account is supported by locals. A shop owner opposite the temple who witnessed the drive, said, “the temple began breaking its piaoo on that same day itself (on 15 March). By the next day, they had completely brought down the piaoo. When the JCB came (on 20 March), they only found rubble. So how can we say the temple was spared?”

Temple trust member Vijay Chhabra said that when he saw the drive, he informed the civic body that he would himself destroy the illegal piaoo (a free service providing drinking water to passersby) before the next drive and promptly deployed men on the job. "Bulldozers usually end up doing more damage, so we decided to remove the encroachment ourselves," he said, adding that the temple had organised a langar (free food stall) on that day.

In any case, on 20 March, the civic body returned with JCB machines and demolished the church steps and cleared whatever was left in front of the temple. However, not before the members of the Christian community again gathered to disrupt it. Rai shared a video of the day on WhatsApp that shows them raising slogans of 'Santosh Rai haye haye' and protesting the demolition.

Photos of the second drive on 20 March (below) show rubble placed outside the temple even as the church steps are intact. According to Rai, this is “proof” that the allegations of the church are false that the temple was spared while they were targeted.