He found him in a classroom and slapped him with the back of his hand across his face.
Mr Allen, and his wife, later met the pupil and his family and he thought things had been resolved.
Yesterday, in the Auckland District Court, Judge Philippa Cunningham said the incident, which other pupils saw, caused concern, and the victim had not deserved to be hit.
However, he hadn't sustained any injury and Judge Cunningham commended the "great character" of Mr Allen.
"[He] has gone out of his way to assist children who might not otherwise complete a school education," she said. "He has poured many years of his life into establishing this school and given unflinching service in return for very little."
A conviction would have made it difficult for Mr Allen to continue his career as a teacher and principal, and Judge Cunningham said this would be out of proportion with the gravity of the offence.
She noted he had undergone counselling since the incident, and highlighted the glowing references provided to her in favour of Mr Allen's being let off the charge.
Ministry of Education executive Katrina Casey said the agency was aware of the matter.
"The school board has stood down the principal and an acting principal is in place. This issue has been reported to the Teachers Council. It is the Teachers Council's responsibility to consider whether or not any disciplinary action should be taken."
A spokeswoman for the Teachers Council said an investigation was under way into Mr Allen and the findings were due to be released in the coming weeks.
When NZME. News Service visited Mr Allen's home yesterday, he refused to come to the door.
He and his school had their names suppressed while the trial was under way, but the suppressions were lifted at sentencing.
Mr Allen's lawyer, Steve Cullen, said the publication of Mr Allen's name and the name of the school would impact on their quest to become a charter school in the future.
The small school had applied to receive charter status, and with it significant funding, but had been declined.
Until last year, the school catered for students from Years 1 to 13.
However, due to funding issues, it now covers Years 1 to 6, and new charter school West Auckland Middle School has been opened on the site for students from Year 7 to Year 10.
There was an indication in court that Nga Kakano kura would try again for charter-school status.
Mr Cullen said he was pleased with the outcome. "I thought Her Honour gave a very considered judgment."
The school is believed to be run by the board of trustees chairman, West Auckland lawyer Bernard Allen, and Te Rangi Allen and his wife.
An application by NZME. News Service to lift the suppressions was granted by Judge Cunningham.
She said there was no evidence that Te Rangi Allen would face extreme hardship if his name was made public because parents of pupils and the school community had shown him great support through the process.
