Israeli's raid Sunday against an Iraqi nuclear reactor risks an estrangement between the Reagan administration and the United States needs crucial help from conservative Arab nations in defusing the crisis over missiles in Lebanon.

Envoy Philip C. Habib's return here yesterday has been greeted with public indifference as U.S. attempts to display an evenhanded approach to the Middle East have been overshadowed by a renewed Arab focus on their longstanding unhappiness over American supplies of sophisticated weapons to Israel.

Western diplomats here privately are worried that Saudi Arabia, a key ally that was humiliated when the Israeli mission flew over its territory without detection, now will be less inclined to exert the kind of diplomatic pressure on behalf of the United States in less friendly Arab capitals such as Damascus.

Even before the Israeli bombing mission, Habib's efforts to have Saudi Arabia, during an Arab League conference here last Sunday and Monday, carry the brunt of plans he was credited with having evolved in his three-week shuttle last month, produced no visible changes on the ground here.Such changes were considered essential to help defuse the crisis over Syrian stationing of surface-to-air missiles in eastern Lebanon in late April.

The best for Habib now appears to be that Israel will forget about the missiles -- which Israeli Prime Minister Menachem Begin has threatened to destroy -- and bask in the glory of the Baghdad raid.,

But in the view of many Arabs, Begin is considered so out of control -- precisely because of U.S. failure to bring pressure to bear on Israel -- that he is fully expected to attack the missiles and Palestinian guerrilla positions, such as the old Beaufort crusader fort in southern Lebanon.

Even the far-from-sure assumption that such attacks will not occur leaves the Lebanese crisis unsolved, with Syria likely to be increasingly adamant in demanding the Christian militias battling the Syrians here break their ties with Israel.

For the Saudis, the raid has raised some new and some longstanding questions about American intentions in the Middle East.

Why, for example, did the United States provide Israel with refueling aircraft since Israel's confrontation-state Arab adversaries are next-door neighbors well within normal fighter-bomber range?

Why did the much-vaunted, U.S. supplied Airborne Warning and Control System sentry planes operating in Saudi Arabia with American crews not detect the marauders?

No doubt there may be good technical rejoinders to all these points. But they are just as likely to fall on deaf ears with the Arabs as has past implicit American acceptance of Israeli arguments that legitimate self-defense is sufficient justification.

Although the United States at times has protested Israeli use of such American equipment as cluster bombs, heavy artillery and aircraft, the Lebanese have witnessed American government impotence in curbing the use of U.S.-supplied weaponry. They are without illusions, despite today's U.S. announcement that a shipment of fighter planes for Israel will be delayed pending a review of possible violations of restrictions on the use of U.S. weapons, that a pro-Israeli Congress would agree to any long-term change in U.S.-Israeli relations.

The acid test of American intentions is expected to be the U.S. posture at the United Nations Security Council debate on the raid, which is tentatively scheduled to begin this weekend.

If the United States fails again to condemn Israel, coservative Arab states feel they will have little choice but to rally around Iraq just as they backed Syria in the missile crisis.

If the United States does condemn Israel, then the Arabs are likely to ask what long-term practical steps the Reagan administration will take to ensure Israeli compliance with what they feel is the spirit and letter of the foreign military sales agreement regulating use of U.S. weaponry.

But U.S. and Israeli fears of unified Arab retaliation effectivedly ended with the separate peace between Egypt and Israel fostered by the Carter administration.

At most, Syria could stage yet another melodramatic -- and doubtless short-lived -- reconciliation with archenemy Iraq. An American Embassy or two could be attacked. Iraq may stage some long-range bomber attacks on Israel or Iraqi-backed Palestinian groups could raid across the border into Israel. U.S. hopes of an anti-Soviet alliance of pro-Western Arab states and establishing a rapid deployment force to protect Persian Gulf oil could be dashed.

But few Arabs believe the ultimate Arab weapon -- another oil embargo -- is in the works in these days of depressed Western economies, oil gluts and prices high enough to encourage alternative energy research.