Two things are at issue in the controversy over the Civil Rights Commission. The first, which has generated most of the political flak, has to do with the qualifications, philosophies and perceived sympathies of the three men President Reagan has named to the commission.

The civil rights leadership, and perhaps blacks generally, consider the nominations hostile to the interests of the very minorities whose rights the commission was created to further. And since there were no vacancies on the six- member commission, the nominations amount, in practice, to firing three commissioners whose views the civil rights establishment finds more compatible.

That issue will be settled in court if, as has been reported, one or more of the fired commissioners challenges the president's action.

But there is a second issue that has to do not with the attitudes and competence of particular members but with the independence of the commission itself. If Reagan's recent action stands, then the commission, which has from its inception been free to make its findings and recommendations without fear of offending the White House, could become just another arm of the administration.

That's the problem Rep. Thomas A. Luken proposes to fix. The Cincinnati Democrat has introduced legislation to create staggered six-year terms for members of the commission and to protect them from firing except for "neglect of duty or malfeasance in office." Luken's bill would also "grandfather in" the present commissioners if the courts rule that their firing was unlawful, or if the new ones fail of Senate confirmation.

Luken's is a commendable attempt to rationalize a situation that, even before Reagan's controversial move, made little sense. Because the commission was conceived as a temporary entity, the legislation creating it did not provide tenure for individual appointees. But it also created what in effect were lifetime appointments. Without fixed terms, the commissioners basically served as long as they wanted to.

These flaws present no problem with a temporary commission. They defy logic with a permanent one. "Just suppose that President Reagan is succeeded by a liberal Democrat who believes in affirmative action and so forth," Luken observes. "The new president would have to choose between keeping the Reagan people, whose views are the opposite of his own, or replacing them with people who represent his own views, which would further erode the independence of the commission."

The staggered six-year terms would fix that, allowing each president to name some commissioners but preventing him from packing the commission entirely with his own people. That provision, together with tenure protection, would help to maintain the commission's congressionally intended independence.

Interestingly enough, the Luken bill is very similar to a proposal put forward some time ago by the White House. It failed when it became clear that, without a "grandfathering" provision, the change to staggered terms would allow Reagan to make the clean sweep he subsequently made anyway.

Unless the courts rule otherwise, the clean sweep--at least this one time-- may be an unavoidable fact. Under the Luken bill, the two most senior commissioners would get full six-year terms, the next two would get four- year terms, and the two junior members would get two-year terms--all of them renewable. But, unless the courts overturn the Reagan firings, all six members would be Reagan appointees.

Thus, while the Luken proposal makes a lot of sense with regard to the future, it wouldn't do a thing for those who fear that the president has transformed the commission into an agency calculated to thwart the prevailing civil rights consensus.