The Israelis had been in secret meetings with King Hussein for three years to coordinate dealing with terror attacks. The raid was entirely counterproductive in that it greatly raised tensions, didn't strike at the real problem (Syria), undermined the only friendly leader and made his future cooperation problematic, and perhaps made war inevitable, which voluminous records show is what the Israeli military wanted.
This is an interesting site reprinting a TIME article about the events in 1966 - it sounds like an atrocity plain and simple. The Israelis moved into a town, detroyed the houses
and the mosque, and ambushed and massacred Jordanian soldiers, who had had nothing to do with the raids on Israel. The raid even managed to unite the USSR and USA in condemnation.
http://www.time.com/time/magazine/article/0,9171,843082,00.html