An unrepentant Robert E. Poli resigned as president of the Professional Air Traffic Controllers Organization yesterday, nearly five months after taking on the federal government in a strike that cost his union money, legal standing and 11,438 jobs.

"I will never, as long as I have a breath left in me, say that the issues for which we struck were incorrect, that we did not have a good reason for going on strike," Poli told reporters yesterday. But he said he believed his presence in office had "become a stumbling block" to any chances fired controllers might have for regaining their jobs.

Administration officials last night said those chances were nil.

"The PATCO union no longer is the exclusive bargaining agent for our employes. . . . We're continuing to rebuild the air traffic control system" with new controllers, Thomas Blank, a Transportation Department spokesman, said.

The dispute began last Aug. 3, when about 13,000 PATCO members, angered over what they said was the government's refusal to improve their working conditions and to grant them more liberal pay and retirement benefits, walked off their jobs at airport towers and flight control centers around the country.

Federal law said they weren't supposed to do that. They had sworn in writing never to strike against the government. President Reagan said he would accept no violation of that oath. He ordered the strikers back to work. About 12,000 initially refused. Most of those who defied the order were fired.

Reagan also unleashed the Justice Department, which filed numerous criminal and civil complaints against the union, its officers and a number of rank-and-file PATCO members. Fines amounted to $150 million. The union filed for bankruptcy.

But the most critical blow was decertification--stripping away PATCO's rights to negotiate for, collect dues from, or in any other way represent its members. That action came Oct. 22 on an order from the Federal Labor Relations Authority, which ajudicates federal labor-management disputes. The union has appealed the decertification ruling, which, nonetheless, stays in effect until a federal court says otherwise.

Throughout the conflict, fired PATCO members kept hoping they would be rehired, despite the administration's repeated denials that it would ever happen. Then, on Dec. 1 and 2, in a modest bid to soothe organized labor's growing discontent with his administration's policies, Reagan gave cause for hope. He said he would consider lifting restrictions barring fired PATCO members from other federal jobs.

The problem was, then and now, that there are few other federal jobs available for fired PATCO members or anyone else. And so, yesterday, in an effort to stifle growing discontent from fired controllers who believe they might be rehired if their top officers stepped down, Poli and his executive vice president, Robert Meyer, resigned.

"Leaving is not easy," said the 44-year-old Poli, who was elevated to the PATCO presidency in a 1980 political coup. He replaced John Leyden, who many union members liked, but considered too soft to lead them into battle against the government.

Poli said yesterday that the only thing he would have done differently would have been to tell his union's story better. He said he goofed by allowing the media to portray his discontent solely as a struggle for $10,000 more a year for controllers who are paid an average annual salary of $33,000. "If that was a mistake, it was mine," Poli said.

He said his professional future is uncertain, that he will continue to speak out when the circumstances warrant it, and that he will finally marry travel agent Diana Kirkpatrick, who has accompanied him to nearly every press conference and congressional hearing since the dispute began.

The two had planned to marry last September. "We'll do it soon, now," Kirkpatrick said yesterday.