Settler groups have repeatedly warned of attempts by the Palestinian Authority to damage Mt. Ebal.
“We order the deletion of the petition after it has been exhausted in its current form,” the court said.
The visit, which was the largest since before the coronavirus pandemic, was held one year after Palestinians torched the shrine.
The basis for the indictments against Rabbi Elishama Cohen and his colleagues and students, the 2005 Disengagement Law, was repealed on March 21.
During the visit, armed clashes broke out between Israeli forces and Palestinians in the area, with three Palestinians injured amid the clashes.
The incident occurred after violence broke out between residents of a Palestinian village and a nearby Israeli settlement.