Justice John Faire ruled the exclusion was illegal, saying the boy had a significant disability which, at times, "manifests itself in behavioural problems which include an inability to react when placed in a confrontational position".
The case follows concerns by IHC about disabled children being suspended for disability-related behaviour, rather than misconduct. The charity is suing the Ministry of Education, alleging that state schools are illegal discriminating against disabled students.
Ms Walters said she was not in a position to comment on the specifics of the Green Bay case, but any school disciplining a student for gross misconduct would only do so if a student had the potential to cause harm to other students.
Schools faced a "juggling game" when allocating teacher aid resources to disabled students, especially when the students were in separate classes.
However disabled students benefited from the socialisation of being included in mainstream classes, she said. "They have to learn to actually get on with other people in a social environment."
Secondary Principals' Association president Tom Parsons said principals were not involved in board of trustees decisions to exclude students, but in general the safety of all students had to be weighed against the rights of individual pupils.
"Unfortunately those two are not always compatible. In instances like this, sometimes the greatest good for the greatest number is paramount as far as (a board's) concerned. Whether or not that is supported legally is another issue."
School resources for educating disabled students in mainstream classes were "finite" and some behaviours could be unpredictable.
"If someone has got behaviour or psychological issues, that doesn't always follow a reliable pattern."
The Green Bay case was complicated, but if gross misconduct had occurred, "justice must be seen to be done", he said. Ministry of Education guidelines stipulate no particular action or behaviour is considered gross misconduct, but it is "never trivial" and must be considered against a high threshold.APNZ