James Gallogly, the head of St Benedict's Catholic Primary school in Wilmslow, was investigated after claims he grabbed an eight year-old with autism and pinned him against a classroom wall last January.
The boy had a history of bad behaviour, and was eventually expelled for allegedly spitting and biting a teacher and throwing a chair at staff.
Mr Gallogly, who is from Stockport, Greater Manchester, resigned his position after an investigation, which was prompted after another member of staff made a complaint against him after witnessing the incident with the boy. Mr Gallogly was subsequently suspended on full pay.
But his resignation has left some parents angry - including the mum and dad of the boy he reportedly pinned to the wall. They wrote to the school asking for him to be reinstated, with the boy's 24-year-old mother telling reporters:
'We wrote a letter in support of Mr Gallogly because we don't believe that he's done anything (wrong).'
Mr Gallogly, who worked at St Benedict's for 12 years, declined to comment on his position, whilst a Cheshire East Council spokesman said he was suspended after 'other issues around his discipline methods' were investigated.
Do you think there is too much ambiguity surrounding discipline at school? Do you think teachers are in an impossible position sometimes?