Murder charges against a man said to be a major organized-crime figure were dismissed yesterday by a State Supreme Court justice who ruled that evidence suggesting that the defendant had prior knowledge of the crime and had been at the scene was insufficient to try him.

The justice, Jerome W. Marks, dismissed the murder charges against Robert J. Hopkins, a former Trump Tower resident who has been linked by law-enforcement officials to the Lucchese crime family, and against Mr. Hopkins's associate, Alexander Rizzo.

Both men are still charged, however -along with 11 co-defendants - with operating a $500,000-a-week illegal betting ring through 100 storefronts in Manhattan, Brooklyn, Queens and the Bronx. Key Evidence Lacking

The decision, released yesterday by Justice Marks at a pretrial hearing in State Supreme Court in Manhattan, threw out the most serious charges in a two-year-long investigation by the Manhattan District Attorney's office. They accused Mr. Hopkins and Mr. Rizzo of ordering the murder of Pedro Acosta, a 37-year-old member of a rival gambling organization led by Cuban emigres.
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In his 22-page ruling, the judge said that prosecutors had failed to connect the defendants with Mr. Acosta's murder outside a Manhattan restaurant in February 1986 or to explain why the killing might have been sanctioned by either Mr. Hopkins or Mr. Rizzo, the purported co-leaders of the Trump Tower ring.

The judge said circumstantial evidence indicating that the defendants - who had just met with Mr. Acosta in the restaurant - might have been aware of the planning of the murder was simply not sufficient to justify taking the case before a trial jury. Both Mr. Hopkins, who has remained free on $1 million bail, and Mr. Rizzo, free on $500,000 bail, have pleaded not guilty to all the charges.

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Mr. Hopkins's attorney, Michael Rosen, said he felt from the beginning that the evidence had been ''stretched'' to accommodate a murder charge.

''This decision reaffirms my faith in the system,'' he said.

District Attorney Robert M. Morgenthau said no decision had been made about appealing the order or submitting the case to another grand jury. Conversation Overheard

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In his ruling, Justice Marks specifically addressed one of the key circumstantial planks in the prosecution's case: a conversation between Mr. Hopkins and Mr. Rizzo just outside the restaurant a few moments before Mr. Acosta was gunned down.
In that conversation, which was overheard by an undercover detective, Mr. Hopkins reportedly said to Mr. Rizzo: ''Hurry up Alex. Let's get out of here before it happens.''

Prosecutors argued to the grand jury that it showed that both men had knowledge of what was about to happen to Mr. Acosta, who had just left the restaurant after a meeting with the defendants.

According to the charges, several members of Mr. Hopkins's group were also seen by investigators outside the restaurant just before the shooting, at 72d Street and Third Avenue, but the gunman escaped.

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Justice Marks said the purported statement by Mr. Hopkins, while sufficient perhaps to raise suspicion, was not enough to carry the indictment to a jury trial.

''The most that one can infer from the statement made by Mr. Hopkins is that he was aware that a crime was about to be committed,'' Justice Marks said in the ruling. ''Knowledge alone of the pending commission of a crime is legally insufficient to render one either a principal or an accomplice