A direct link between the Khomeini regime and shadowy, hostage-taking Hezbollah Shiites in Lebanon points to an Iranian intelligence unit with a known address in Tehran as the control point for operations that -- most recently -- resulted in the June 17 seizure of American reporter Charles Glass.

The new evidence indicates that Tehran exerts far tighter control over Hezbollah's operations than frightened Western governments have considered likely. Up to now, suspected links between Tehran and Hezbollah strongholds in the Beirut slums, with supporting elements in the Bekaa Valley, have been tenuous -- but the People's Mujahedin, the largest anti-Khomeini resistance organization, has now pinpointed Tehran's control.

The Eighth Branch of Iran's feared intelligence agency now appears to be in charge of hostage-taking operations in faraway Lebanon, under the control of Parliament speaker Hashemi Rafsanjani. This is the same Rafsanjani who was billed as the ''moderate'' Iranian leader whom U.S. operatives in the arms-for-Iran affair said would free American hostages and take power after Khomeini.

The prospect of Western intelligence agencies proving that the Khomeini regime is indeed the real trigger-point for seizing hostages in Lebanon gives President Reagan new ammunition to support his Persian Gulf strategy. A key congressional complaint is that Reagan's reflagging plan for Kuwaiti tankers favors Iraq at Iran's expense. That dubious argument collapses with direct Iranian complicity in seizing American hostages in faraway Lebanon.

''If Iran does slug us in the Persian Gulf,'' a top House Democrat told us privately, ''a proper retaliation target would be the place in Tehran that controls Hezbollah hostage operations in Lebanon.'' Real U.S. neutrality in the Iran-Iraq war, he said, could not survive a finding of Iran's direct responsibility for anti-American terrorist acts by Hezbollah.

The anti-Khomeini People's Mujahedin, savaged by the State Department until early this year as a ''terrorist'' organization, is now in possession of fascinating details about Khomeini's remote control of Lebanon terrorists. Its penetration of Khomeini security organs portrays a highly developed, well organized operation that so far has been unknown to the West.

As one example, electronic communication and mail are not allowed between Tehran and Beirut. Orders are dispatched by courier, often without written documents. These orders emanate from a nondescript building on Pasdaran Street under control of a director who was sent on a 10-day assignment to Lebanon in early June. There is speculation here that this journey was probably connected to the kidnapping of Glass and the son of the Lebanese defense minister (who was soon released) on June 17.

The reported ''coffin flight'' of two other American hostages, said to have been anesthetized, wrapped in white shrouds, hidden in coffins and flown to Tehran, may also have resulted from that early-June trip. American intelligence officials say they have no evidence one way or the other.

But there have been persistent rumors that the two Americans, reported to be chief Associated Press Mideast correspondent Terry A. Anderson and American University dean of agriculture Thomas M. Sutherland, will be put on trial in Tehran.

That would show the far reach of Rafsanjani, a key contender for post-Khomeini power. Rafsanjani was hurt by premature disclosure of the U.S. arms sale last November. If the two American hostages were put on trial by a revolutionary court in Tehran at his instigation, Rafsanjani's stock would unquestionably rise. The Khomeini regime may also believe that since its dealings with Oliver North's cabal of underground U.S. operatives actually produced arms for hostages, the threat of trial might yield new dividends from the Reagan administration.

Cool Capitol Hill heads knock the props out of this argument. The sensational disclosures of the Iran-contra hearings, together with the intensifying naval warfare by Iran in the Persian Gulf, have reversed the gradual drift in Congress away from the anti-Iranian passions that followed the 1979-1981 U.S. embassy hostage crisis.

Revelation that the Americans victimized by kidnapping in Lebanon have been individually selected by a secret Khomeini intelligence bureau in Tehran would add fuel to this reversal. Even the pro-Israel congressional bloc that objects to U.S.-Arab dealings might ask itself whether Khomeini really deserves anything approaching strict neutrality from the United States.