WHEN Georgetown's basketball coach walked off the court at Saturday's contest with Boston College, adoring fans gave him a standing ovation. Funny thing is, the game hadn't even started.

John Thompson had pledged to boycott the game as a protest against NCAA Proposition 42, a stringent new regulation enacted last week to prevent the academically deficient from competing in intercollegiate athletics.

Proposition 42 closes a loophole in the 1983 NCAA Proposition 48. Proposition 48 required students to post a 2.0 GPA in "core" high school courses and to get a combined score of 700 on the SAT or a composite score of 15 on the ACT to be eligible to play sports.

The loophole in the 1983 rule allowed "partial qualifiers," students with a 2.0 high school GPA who didn't make the requisite standardized test score, to attend college on athletic scholarships for one year. Although partial qualifiers lost one year of athletic eligibility and were not permitted to compete in their first year, they had a chance to gain eligibility by posting a 2.0 GPA during that year.

THE problem with this loophole is that it provided a tremendous incentive for unscrupulous institutions to cheat. High schools were under pressure to give academically deficient athletes a C average so they would be eligible for athletic scholarships. Dishonest colleges could make partial qualifiers eligible by enrolling them in gut courses. So Proposition 48 only hurt the schools that were honest enough not to take advantage of it.

University of Georgia instructor Jan Kemp was dismissed from the faculty after complaining about the coddling treatment given to partial qualifiers in the school's remedial studies program. She sued the university and received $ 1.8 million in a negotiated settlement.

In response to the controversy, Georgia President Fred Davidson ordered the university's coaches not to accept any more partial qualifiers. Because this rule would place Georgia's teams at a competitive disadvantage, the coaches successfully lobbied the Southeast Conference (SEC) to adopt the regulation for all of its member schools.

SEC Commissioner Harvey Schiller then petitioned the NCAA to close the partial qualifier loophole for all colleges. Last Wednesday at their annual convention in San Francisco, the NCAA adopted Proposition 42 by a 163-151 vote.

THE rule sparked massive protests from college coaches. At the center of the controversy is the alleged racial bias of the rule: 83 percent of the approximately 700 partial qualifiers sitting out under Proposition 48 are Blacks.

Temple's head basketball coach, John Chaney, called the NCAA a "racist organization." Dale Brown, head basketball coach at Louisiana State, said, "What they're saying is, 'We have a colored fountain here, a white fountain there. We'll allow you to drink out of the white fountain if you pass this test.'''

Georgetown's Thompson complains that Proposition 42 discriminates against Blacks because it deprives only the disadvantaged of the means to get a college education. Presumably, wealthy, academically deficient athletes will still be able to pay their own way and sit out a year under the partial qualifier rule.

PROPOSITION 42 does discriminate against the economically disadvantaged--but so does American higher education in general. Some academically deficient athletes will certainly find it more difficult to attend college--but certainly no more difficult than intelligent, disadvantaged students who can't shoot baskets. Athletes affected by Proposition 42 will still qualify for Pell grants, Guaranteed Student Loans and other financial aid available to their non-athletic counterparts.

The complaint of the bias against disadvantaged students is transparently cynical. This committment to equal opportunity for students of all socioeconomic background extends only to athletes. What coach has ever offered to share athletic slush funds with a brilliant, poverty stricken klutz?

Besides, granting a college scholarship to an athlete who is incapable of college work does him no favor. He is herded through college, sheltered from serious work that might threaten his GPA and athletic eligibility and exploited for his ability to shoot free-throw or catch touchdown passes.

As soon as an athlete's NCAA eligibility expires, the same coaches that lured him with the improbable prospect of a professional career and so generously provided him with an athletic scholarship simply forget about him.

Even worse, sheltering academically deficient students throughout high school and college gives them the destructive perception that their athletic ability will always grant them success without academic achievment. Except for the miniscule number who become professionals, college athletes will eventually discover that athletic ability alone is not a ticket to success in the rigorous real world.

Perpetuating the cruel hoax that academically deficient athletes are legitimate college students does them a terrible disservice. Proposition 42 merely exposes that unpleasant truth.