Yes, there was something to be gained.
At that time, the US was not that supportive of Israel and certainly not of any offensive action by Israel; at the time we had actually embargoed Israel. The USS Liberty was a “technical research ship,” i.e. a spy ship.
On June 7&8 the Israelis were planning an attack against the Golan Heights. The Israels did not know how much SigInt had been collected by the USS Liberty, or what type. But they may have feared that if the intelligence collected by the Liberty were provided to the Arabs it could cause the attack to fail disastrously.
The threat was removed when the USS Liberty was crippled. The attack on the Golan Heights was a success.
That is a possible motive for a deliberate attack on the USS Liberty.
I would say that Israel already had proof that information was being given to the Arabs and the official story saves US a whole lot of embarrassment.
Is that a conspiracy theory, or a mockery of conspiracy theories? It's hard to tell.