According to a declassified CIA report IDF units misidentified the Liberty as the Egyptian El Quesir, which it slightly resembled. The Ras Sedr massacre was alleged to be two or three dozen POWs (which is bad enough!), not 2000. Many Egyptian POWs were told to walk back to their lines, the IDF only having capacity to take officers into custody to exchange for downed IDF pilots. Many of those likely didn't survive the trek through the Sinai.

It's certainly possible that IDF commanders ordered the attack on the Liberty in fear it had overheard evidence of the massacre, but attacking one's key (& virtually only) ally in such a circumstance is a very big & reckless step to take.