I'm not sure that you can say that Israel was an 'ally' of the US during that period in history. Most of the weapons systems in the IDF inventory were either French (aircraft) or British (tanks). The American-built equipment that they had was largely purchased on the world arms market or smuggled. Also, Eisenhower had forced the Israelis out of Suez in '56 when he yanked support from the French/British component of the operation to regain the Suez Canal.
Putting it all together, Israel might have had a motive to 'blind' US intelligence to their strategic intentions. I go back & forth about the "Liberty Incident", but I'm not prepared to dismiss the possibility that it was intentional.
There have been some first hand accounts by Liberty’s crew of how the Israelis first scouted the ship and then attacked despite desperate attempts by the crew to identify the ship as U.S.
These accounts convinced me. I don’t think I have a tin-foil hat mentality, but simply a realistic viewpoint of the perceived needs of Israel to maintain their security. These needs aren’t necessarily the same as the desires of the U.S. government.
Our Government’s ‘official’ accounts and investigations are less convincing because they take into account the diplomatic interests of the government in preventing full disclosure.