NOW THAT Anne Burford has departed, the

questions about the Environmental Protection Agency's future move up one level. What does President Reagan think about the EPA, and what does he want it to do? Does he still think there's nothing wrong that more budget cuts and deregulation won't cure? Probably not. The past several months may have suggested to him, and to the people around him at the White House, that they are going to need different kinds of people to run the agency. The main issue now is not Mrs. Burford, or Rita Lavelle, or James W. Sanderson. It is presidential intention concerning toxic pollution and health protection.

The EPA was in several kinds of trouble before the Reagan administration ever arrived--not scandal, but a deeper intellectual trouble. Congress had written a lot of law in absolute and sweeping terms that were inconsistent with scientific understanding of the subject as it was developing. The law gave the agency little guidance in balancing pollution control against economic cost, even in the cases where costs were exceedingly high for negligible gains in health protection.

Many of the basic laws--the Clean Air Act, for one--had established fixed schedules of permitted levels of specified pollutants. As time passed, it had become clear that some of the levels were too high, others too low, and some of the most disquieting pollutants were either not on the list or incorrectly defined. Ten years of regulatory experience had shown that its foundation of basic science was not strong enough for the legal structure that the agency was trying to build.

The Reagan administration made most of those defects worse. Its first attempt at revising the Clean Air Act called for a general retreat on a scale that immediately created a stalemate with Congress. The administration's budget cuts further diminished the agency's scientific capabilities. Sometimes the agency simply declined to enforce legal requirements. Far from winning the unanimous support of industry, the administration began to hear from the companies that had spent millions to comply with the law only to see their lagging competitors rewarded with extensions and exemptions. The administration slowly began to see that support for pollution enforcement is broader than it had thought. The dioxin case in Missouri was a compelling reminder that pollution is dangerous.

A prominent resignation like Mrs. Burford's always gives a president an opportunity to recoup a defeat and set new policy. In several important places--at the top of the State and Energy deparments, to name two--Mr. Reagan's second thoughts have been a notable improvement on his original choices. If ever there was a case for careful second thoughts now, it's the EPA.