Someone here explained that they did not storm anything and that it was apparently allowed per the law. I am yet to find that post. So I dont think any resulting violence falls under the terrorism category. However, there were other settler violences that have resulted in needless deaths. Those are definitely terrorist attacks and yes, I support putting one right between the eyes for those assholes too.
As far as I know non-Muslims are allowed to visit the Al-Aqsa mosque, the third holiest site in Islam, under a "status quo" agreement, but are forbidden to pray there.
As the actual site is also an extremely holy one for Jews, known to them as the Temple Mount, located above the Western Wall, and where King Solomon built the first Temple 3,000 years ago, some Jews do try to pray there, which really pisses off the Muslims there. Also Israelis have sometimes tried to prevent Muslims from praying there.
So if large numbers of Jews converge on the site and try to pray there during Jewish holy days the Israeli police get involved to stop the clashes between the Muslims and Jews at the site, and may likely side with the Jews.