A few years ago, Howard University president James E. Cheek launched a program designed to help the university's school of law recover its once-shining reputation. A few days ago, the law school suffered a staggering blow to its reputation and quite possibly to its survival. The unlikely source of that blow: James E. Cheek.

Cheek, overruling the academic judgment of the law school faculty, ordered the graduation of nine students who failed to meet graduation requirements -- an interference that prompted the resignation of the law dean and may have put the school's accreditation in jeopardy.

In an extraordinary public exchange at Saturday's graduation program, the departing dean, John T. Baker, defended his adherence to "the highest standards of excellence," while class president Darcel Clark expressed delight that her class had played a role in getting rid of Baker, who, she said, "has not been sympathetic to students." They also exchanged shots over how "black" the law school should be. It was all very interesting and very much beside the point of the school's immediate problem: its recovery and survival.

It may not seem particularly unusual for Cheek and his vice president for academic affairs Michael Winston to overrule Baker, their subordinate and a newcomer to the Howard faculty. But the canons of the American Bar Association committee that oversees law school accreditation are explicit on the point that academic decisions and certification for graduation are the province of the law faculty, operating within the bounds of university policy, not the administration. Some observers familiar with ABA procedures are fearful that Cheek's interference may prompt an unfavorable review of the law school's accreditation.

Cheek himself seems to be aware of the potential problem. A press statement issued Friday was careful to say that the 13 students who appealed the law faculty's determination that they had fallen short of gradution requirements were seeking "relief from actions . . . that were, in their view, inconsistent with university policies." The hope, apparently, was that the ABA committee would view the controversy as a matter of university policy rather than of academic oversight.

Most of the 13 petitioners, nine of whom graduated Saturday, had either fallen short of the 88 credit hours required for graduation or had not passed a required course. At least one of the 13 was allowed, over a law faculty decision to the contrary, to sit for reexamination after failing the first time. The question is whether those administration decisions constitute "policy" or academic interference.

Howard's law school has, in recent years, been a victim of a "skimming" that has seen most of the best-qualified black law applicants going to more prestigious law schools. One result is that Howard's law graduates have had difficulty passing state bar examinations. Reliable statistics are hard to come by, but in Maryland, which keeps school-by-school data, only 13 percent of Howard's graduates had passed the state bar between 1981 and 1985, compared with 65 percent overall. Last year, approximately 65 percent of the applicants passed the D.C. Bar Examination. Less than 15 percent of Howard's graduates passed.

It was partly to reverse that trend that a new plan of action was undertaken in 1982, reportedly with some success. Wiley A. Branton Sr., the civil rights lawyer who left the deanship for private practice a year ago, and the recently resigned Baker were hired as a part of the effort to improve the law school's performance. The latest controversy places that effort in jeopardy.

It was an avoidable state of affairs, and it should have been avoided. Howard, even in the face of "skimming," is capable of turning out eminently competent lawyers. But to do so requires facing a reality that Cheek finds uncomfortable.

The law class president praised Cheek for his "sympathy." But sympathy without academic rigor is a disservice that threatens to continue the record of having bright young students spend seven years in preparation for a career that many of them are unable to pursue.

The issue is not whether Baker or Clark scored more points during Saturday's exchange. Baker, himself a Howard law graduate with outstanding credentials, will return to teach law at Indiana University. But Howard's law graduates, even those who manage to pass the bar, are likely to find themselves bearing the taint of having attended an overly permissive law school, giving ammunition to those law firms that have been reluctant to hire Howard graduates.

There can be little doubt that Cheek, for all his sympathy, has delivered his law school a crippling blow. The question is, can it recover?