The first charge was withdrawn by police last month after Samuels pleaded guilty to a similar charge of organising a protest gathering at Memorial Park on October 30.
Samuels was sentenced in the Tauranga District Court today by Judge Louis Bidois and sought a discharge without conviction.
His lawyer Rachael Adams filed written submissions arguing that a conviction for her client would be out of all proportion to the gravity of his offence, the court heard.
Police prosecution took a neutral position on the application.
Judge Bidois agreed to discharge Samuels without conviction and described the pastor's offending as "misguided loyalty" and a mistake in judgement.
In terms of the offence, the protest gathering had put lots of people at risk of getting Covid-19 and lots of people have died from the virus, the Judge said.
Judge Bidois said he also took into account that Samuels' was a first-time offender before the court and had accepted responsibility for "his mistake", plus he had clearly made a significant contribution to the community both in his role and in the wider community.
Judge Bidois said a donation to a charity was clearly warranted, and he ordered Samuels to pay $750 to the Homes of Hope Charitable Trust within seven days.
Samuels suggested the Homes of Hope charity.
He and his lawyer both declined to comment outside the courtroom.