After more than six years of legal proceedings, the decision was handed down by the Israeli Special Appeals Committee for Land Seizure under emergency law in late April.
"This solution is still unacceptable for us because the school will be encircled on three sides by the wall," said Anica Heinlein, advocacy officer at the Society of St. Yves, which has been representing the Salesian Sisters of Cremisan, who operate the school and an after-school program for 400 children.
"The street leading to the school will go along the wall and will have a heavy military presence. Whenever the gate is open or there is some security concern, there will also be a military presence. Also you wouldn't want to send your children to school with those conditions."
The Israeli separation barrier is a series of cement slabs, barbed-wire fences and security roads that would effectively separate Beit Jalla from two Israeli settlements, creating a strip of land that could be used for expansion and the eventual joining of the settlements.
The plan, which leaves the convent and school on the Palestinian side of the wall, will also cut off the Salesian sisters' convent from the neighbouring Salesian male community, which will be on the Israeli side of the wall. Though a gate is to be placed in the wall to ease movement between the two communities, Heinlein said that this is a violation of religious freedom.
The Salesian men "come on a daily basis to the nuns to celebrate the holy Mass; this is not freedom of religion," she said.
The wall will also put limitations on two religious processions traditionally celebrated every year by the residents of the neighbouring village of Beit Jalla, she added.
The gate is designed to also allow farmers and landowners access to their lands on opposite sides of the wall, though they will need permits to reach them.
Heinlein said the Society of St. Yves is considering taking the case to the Israeli High Court.