A defiant Edwin Meese III, refusing for long months to resign in the face of criticism and criminal investigations into his conduct, goes out with his head held high after a special prosecutor refused this week to indict him.

A 14-month investigation produced an 830-page report that sources said found no evidence of criminal activity by the U.S. attorney general. The still-secret report will be released later this month.Meese, who said he would not be hounded out of office by false accusations, had grimly stayed on the job in the face of calls for his resignation--calls from political foes and from friends who said his presence was hurting the administration. There was no way that President Reagan would ask for the resignation of his long-time friend and adviser.

But when the news came that the special prosecutor failed to find basis for criminal charges, the attorney general said his reputation had been cleared and he was now free to resign--effective late July or early August.

This way, his personal reputation is clear, yet he can ease some strains for the president and others by leaving a few months before the Reagan administration comes to an end.

Accusations against Meese have been many, dating back five years when Meese was a White House adviser before beging named attorney general. Such accusations frequently involved influence peddling, jobs given to his family members, unreported loans, conflicts of interest, deals with Wedtech Corp., and involvement in the Iran-Contra affair.

While Meese may have been careless in some of his associations and actions, there is a lesson in his exoneration of criminal behavior. Accusations are one thing, guilt is quite another. The presumption of innocence is often forgotten in a swirl of complaints and rumors.

However, for a political figure, suspicion can be deadly. And repeated problems, particularly involving and nation's highest law enforcement official, cannot be lightly dismissed.

Meese's departure, no matter what the circumstances, is bound to bring a breath of fresh air to the Justice Department, where Meese was having trouble filling important posts because of clashes with other Justice officials.

What this will do to Harold G. Christensen, the Salt Lake lawyer recently appointed as No. 2 man in the Justice Department, is unclear. Reagan said that choosing a successor to Meese "will come later."

One immediate effect of Meese's resignation will be to diminish the political liability that Meese has been to Republican presidential candidate George Bush. Democratic candidates had been tarring Bush with the Meese brush. Both the prosecutor's report and Meese's departure wil remove much of that criticism.

This is a good time for Meese to leave. He goes out with his personal honor essentially intact, and at the same time, gives the Justice Department and the administration a chance to smooth over his rough tenure.