WHEN THE UNIVERSITY of South Florida declared late in 2001 that it meant to fire tenured computer engineering professor Sami Al-Arian, he became a cause celebre of academic freedom. Mr. Al-Arian had long been suspected of raising money for Palestinian Islamic Jihad, a terrorist group that conducts suicide bombings against Israel. Yet even as the feds disclosed their continuing investigation related to Mr. Al-Arian, many were quick to label the case a post-Sept. 11 witch hunt. They were reacting partly to the university's poor handling of the matter; it initially blamed the disruptive atmosphere created by his presence, not his alleged terrorist links. But Mr. Al-Arian's defenders also ignored the possibility that their man was actually a terrorist. The faculty union filed a grievance alleging discrimination, among other things. Georgetown University Islam scholar John L. Esposito canceled a scheduled speech at USF, saying it was impossible for him to appear "at a university that so clearly violates the academic freedom of one of its professors." The American Association of University Professors threatened to censure USF if it fired Al-Arian, after its investigating committee found the charges "insubstantial" and determined that "grave issues of academic freedom and due process" were at stake.

Last week, a federal grand jury issued a lengthy indictment of Mr. Al-Arian and several others. They are innocent until proven guilty. But the government is alleging far more than that Mr. Al-Arian was a terrorist fundraiser or a political sympathizer with Islamic resistance to Israeli policies. It contends, with considerable supporting detail, that he was a top official of Islamic Jihad. According to the indictment, he managed its money, held the wills of would-be suicide bombers, disseminated statements claiming responsibility for attacks, helped formulate policy on behalf of the organization, and was in regular covert contact with its general secretary, spiritual leader and other operatives. If these allegations prove true, Mr. Al-Arian -- far from a victim of a new anti-Muslim McCarthyism -- will rank among the more important terrorists ever arrested and prosecuted in this country.

The government's long-running investigation, like the university's actions, has been troubling at times. Mr. Al-Arian's brother-in-law, Mazen Al-Najjar, was held on secret evidence for nearly four years while the government pursued his deportation. But the indictment suggests that many people were too reflexive in their disbelief that an urbane, politically active professor -- one who had been to the White House and who regularly talked to journalists -- could be a genuine terrorist, and in their automatic assumption that he must be a victim of university railroading and FBI abuses.