The 11-year-old boy has been back at Llantwit Major comprehensive school in south Wales since an independent appeal panel said in November that he should be reinstated.
Union leaders say that the boy would not have been returned to school if tighter rules, introduced in England in January, had been in force in Wales.
"If we'd had the same rules as England, this would not have happened," said Tim Cox of the National Association of Schoolmasters Union of Women Teachers. "But ideally we'd like the appeals panels scrapped."
New guidance for England says panels should balance the interests of the excluded child against those of the rest of the school community and should not reinstate pupils excluded for serious violence or carrying an offensive weapon.
In addition, appeal panels in England can now rule that a pupil should not have been excluded but that relationships have broken down so far that he or she should not be returned to the school.
The Welsh Assembly is to consult on similar changes in March. Abolishing the appeal panels is thought to be ruled out on human rights grounds.
The shooting happened last September, only three weeks after the boy started at the school. He says he hit his sociology teacher, John Alter, by accident and that he was aiming for people's legs.
Michael Norton, the head, permanently excluded the pupil and his decision was backed by the governors. After he was reinstated by the appeal panel, NASUWT members voted not to teach the child. But they suspended their action at the start of term to enter talks with the school and the local authority.
The boy is being educated in the school's behaviour support unit and will gradually be returned to ordinary classes.