He is deceptively baby-faced and unfailingly polite. But to the people who have planned and nurtured President Carter's foreign policy, the sight of John Carbaugh hustling through the corridors of the State Department is a phenomenon comparable to a vandal running loose inside the walls of Rome.

Carbaugh, 35, is an aide to arch-conservative Sen. Jesse Helms (R-N.C.). When he surfaced last week as part of the team arranging the Republican takeover of State, it was a vivid reminder that, despite the aura of mutual civility and cooperation characterizing the transition, the shift from Jimmy Carter to Ronald Reagan is going to mean some abrupt about-faces in American foreign policy.

For the past four years, Carbaugh, who unabashedly relishes his reputation as a "bomb thrower," has been among the most active practitioners of the guerrilla warfare waged by neoconservatives against the Carter administration's most cherished goals.

During the bitter fight over Senate approval of the Panama Canal treaties, Carbaugh was an interpid leader and planter of news items aimed at discrediting the treaties and their supporters. Later, he used his myriad press contacts to spin out the tidbits of information that helped make the Soviet brigade in Cuba an issue of acute embarrassment to the administration.

Along the way, Carbaugh and a colleague from Helm's staff made headlines when they flew to London in September 1979 in what State Department officials charged was an attempt to impede the sensitive negotiations on black majority rule for Rhodesia. In league with his rightist allies on Capitol Hill and elsewhere, he also has pursued an unceasing array of skirmishes against such top-priority administration policies as the strategic arms limitations treaty (SALT II), the effort to cooperate with leftist forces in Central America and the Caribbean, and the application of human rights pressures on repressive, right-wing regimes.

That record is a source of considerable dismay to Carter administration officials who see Carbaugh's presence on the transition team as a symbolic warning that the Reagan people can't wait to take a blow-torch and meat ax to everything they have done over the last four years.

Carbaugh, though, insists that isn't necessarily the case. In an interview yesterday, he said: "If security and foreign policy is an entity of 100 percent, the disagreements between us involve mainly only 3 to 5 percent of that entity. In the few days I've been at the State Department, I've been very surprised to realize the tremendous amount of agreement that exists between those who are leaving and those coming in."

In addition, Carbaugh noted, he is only one among 15 members of a transition team whose job "is not to make decisions about policies or personnel but to take an inventory of the major outstanding issues and the people and approaches being used to deal with them so this information will be available to the decision makers on Reagan's staff."

Finally, he stressed that he is not at State as the representative of Helms and his hard-line positions. "Jesse Helms speaks for himself. I still work for him, and follow his lead on Capitol Hill. In the transition, I follow Gov. Reagan's lead. That doesn't mean there's any real conflict, though, because the governor and the senator both have pledged their allegiance to the principles of the Republican Party platform."

But, while what he says is true as far as it goes, Carbaugh's soothing words don't tell the whole story. The 3-to-5 percent "area of disagreement," that he cites involves most of the Carter administration's major policy initiatives, and many of them fall within those areas that Carbaugh has staked out as his special concerns in the transition -- human rights, Latin America, Africa and the Far East.

Also, while it's true that Carbaugh represents only one of the many factions jockeying for influence with Reagan, it's clear that he is not without clout in the transition process. Sources familiar with its workings say that's due partly to the backing of Helms, an early Reagan supporter to whom the president-elect owes several due bills, and partly to what one calls "Carbaugh's extraordinary adrenalin level."

According to the sources, the State Department transition team, headed by Robert Neumann, a scholarly and courtly former ambassador to Afghanistan, is still in a shakedown phase. As one source says, "Some members have hardly stuck their noses in the door, some have picked out one area and concentrated on it, and some are all over the place. Of those in the latter category, you might say Carbaugh is the busiest boy on the block."

Although Carbaugh insists that he knows nothing about it, there is already considerable speculation that Helm' patronage will secure for him the job of assistant secretary of state for congressional relations or possibly assistant secretary for Latin American or African affairs.

Despite the disclaimers about the transition team's limited writ, it will be making recommendations about policies and personnel. While it's by no means certain that the policies advocated by those whom Carbaugh represents will be adopted by Reagan and whoever he selects as secretary of state, there's no question that they will have to pay respectful attention to their views -- particularly in the key area of choosing policy makers acceptable to the Republican right.

Carbaugh, while refusing to discuss these issues in detail, left little doubt about what his recommendaitons would be. In his view, he said, the United States has to take "a cold, hard look at southern Africa" and seek ways to influence South Africa's white minority government through friendly persuasion rather than confrontation.

On Latin America, he said, "If the United States is going to be a world leader, we have to clean up our home ground." That, he stressed, means reversing the Carter administration's "flirtation " with leftist forces in El Salvador, Nicaragua and the islands of the Caribbean.

The United States, he added, has an obligation to pursue a worldwide policy of better human rights. But, he stressed, "it has to be kept in proper perspective, and the new secretary of state should look carefully at the extent to which it has built a self-perpetuating, entrenched bureaucracy and the extent to which it has achieved a pervasive influence within the State Department."

Carbaugh lauded the cooperation he has received from Carter appointees at State and said: "We have to be careful to look at the human factor and see where these people are coming from. They're people who, in effect, gave birth to a baby and who have raised it lovingly for four years. Now we can't just throw their baby out with the bath water. There has to be some continuity, and where change is unavoidable, it should be gradual wherever possible."

Still, he concluded, "when you change parties and philosophies, there has to be a change of people and policies. In the end, the State Department must be stamped with Reagan's imprimatur. That's the bottom line."