Kennedy did not order the assassination of Diem. There is no evidence the U.S. sought his death. His political support was collapsing in Vietnam and his position became untenable. His enemies within Vietnam killed him.
Put down the Chomsky and Zinn books.
There is no shadow of a doubt that the coup against Diem led by Big Minh was backed by the Kennedy administration. The possibility of Diem’s death was understood and so some effort was made to make him abandon his role and South Vietnam. Diem refused to abdicate.
The real collapse was the vacuum created by the anti-Diem coup and the instability of South Vietnam for the next two years. Yes, their were protests against the Catholic Diem but he enjoyed more support than his successors. The Kennedy brothers wanted somebody that would play ball the Kennedy way and thus financed the coup against Diem by the squish of all squishes Big Minh.