Marshall was opposed to Israel's independence because he feared that it would lead to regional unrest and war. He accused Truman of favoring the recognition of Israel so that he could secure the Jewish vote for the upcoming election, placing domestic political considerations above matters of international security. The entire State department, for the most part, was similarly opposed to recognition of Israel. But Marshall was the only one whose dissent arguably rose to the level of insubordination.

This first hand account from former Special Counsel to the President, Clark Clifford goes into more detail:

http://jcpa.org/article/president-truman%E2%80%99s-decision-to-recognize-israel/

Pay specific attention to the section "Secretary of State Marshall Threatens President Truman". The money quote:

Lovett joined the attack: “It would be highly injurious to the United Nations to announce the recognition of the Jewish state even before it had come into existence and while the General Assembly is still considering the question. Furthermore, such a move would be injurious to the prestige of the President. It is obviously designed to win the Jewish vote, but in my opinion, it would lose more votes than it would gain.” Lovett had finally brought to the surface the root cause of Marshall’s fury – his view that the position I presented was dictated by domestic political considera­tions, specifically a quest for Jewish votes.