LAST WINTER, when the Federal Trade Commission began its investigation of television advertising aimed at children, it looked as if we were about to witness a classic confrontation between new consumers' groups and the old business establishment. But the case has taken a curious twist with the judicially-ordered disqualification of FTC Chairman Michael Pertschuk from further participation in it. What started as an argument over the wisdom of establishing federal rules on the amount and kind of advertising that can be directed at small children has now become, as well, a vehicle for questioning the propriety of a reformer serving as a regulator.

Mr. pertschulk has been quite outspoken about this particular case. He has left little doubt in our mind - or in the minds of many others - that he believes children need more protection than they are now getting from certain kinds of advertising, especially from those that hawk highly-sugared products. Thus it was not a surprise that Federal Judge Gerhard A. Gesell ruled Mr. Pertschuk had made up his mind about how the FTC should decide the case before the evidence was in.The judge took the next, obvious step of barring Mr. Pertschuk from helping his colleagues on the commission to make their decision.

On the surface, Judge Gesell's ruling is clearly right - it does seem basically unfair to have an advocate of one particular view serving on a commission that must judge between that and competing views. But the implications of the ruling are troubling. If Mr. Pertschuk was disqualified because of his advocacy on television advertising, was it proper for an advocate of airline deregulation to sit on the Civil Aeronautics Board? Or for an advocate of deregulating the trucking industry to sit on the Interstate Commerce Commission? Indeed, the trucking industry is now talking about attempting to force the disqualification of ICC Chairman A. Daniel O'Neal in several major cases because of his views on deregulation.

The problem, of course, is trying to distinguish between the legislative and judicial functions of the regulatory commissions. If Mr. Pertschuk was acting was acting as legislator, who ever questioned the right of a member of Congress to vote on a particular bill because he had forcefully supported?

This mixing of roles has troubled some people ever since regulatory agencies were established. The agencies, says William F. Bagley, who recently resigned as chairman of the Commondity Futures Trading Commission, are the marshals as well as the judges. He urged President Carter to support legislation to strip the quasi-judicial functions from the agencies and create a special regulatory court. But woudl a court - of any kind - be the proper place in which to handle the television advertising case, a case that involves matters of public policy?

It may be that Mr. Pertschuk was simply too aggressive in pursuing a particulary industry - or simply talked too much - once he shifted from his role of initiator of FTC investigations to judge or rule-maker. Or it may be that the courts will distinguish between the role of a regulator in a specific case, like children's television, and in a general category of cases, like trucking deregulation. Either way, Judge Gesell's ruling suggests that those who become regulatory commissioners with the intent of making sweeping changes have a delicate line to walk if they are not to find themselves ordered to the sidelines, like Mr. Pertschuk, when the ultimate decisions are made.