Ayatollah Ruhollah Khomeini, in the face of growing signs that his support is warning, warned today that Iranians who reject his Islamic rule will be "destroyed by the same fist that destroyed the shah."

Addressing a rally in the holy city of Qom, Khomeini called his critics empty-headed intellectuals imbued with Western valued that had caused them to stray from the truth path of Islam.

"I advise you to write in favor of Islam," he said. "Sectors that oppose Islam should take our guidance. Otherwise, they will be destroyed by the same fist that destroyed the shah. Their ideas and speeches should be in keeping with the masses, or else they should go."

Khomeini's harsh words reflected irritation at growing protests against his authoritarian policies and application of Moslem strictures to the Iranian society that Shah Mohammad Reza Pahlavi had tried to westernize.

In rapid succession, the Iranian Bar Association condemned efforts by Khomeini's encourage to drop plans for an elected consituent assembly, fighting flared between autonomy seeking Arabs and Khomeini forecs, the liberal National Democratic Front criticized Khomeini personally and the National Iranian Oil board of directors resigned.

In an unrelated but nonetheless troubling development that may have contributed to Khomeini's anger, the government reported that four Iraqi jets pursued Kurdish guerrillas across the border yesterday and bombed at least two villages in Iran's West Azerbijan Province.

The government statements were the first official report of an Iraqi air strike against Kurdish rebels since Iran's revolutionary government took power in February. Tehran newspapers reported then that 15 people were killed in such an incident, but it was never confirmed by the government.

There was no indiction of what prompted the Iraqis to mount the reported strike inside Iranian territory. Iraq's Kurds, as far as known, have been quiescent since their revolt was crushed in March 1975 following agreement between the shah and Iraq s Baathist government to seal off the border and prevent access to the Iranian Kurdish villages that the Iraqi rebels had used as staging areas and havens.

Khomeini made no reference to the attack in his Qom speech, the highlight of a series of rallies in cities and towns across the county called by the ayatollah in an apparent effort to counter the protests against his rule.

Indicative of his waning authority, however, was the relatively light turnout at today's main rally at Sepah Square in south Tehran. Reporters climbed to the roof of the 15-story telecommunications building to watch the crowds gathering below. They estimated the number of demonstrators in the square - two thirds full - and in surrounding streets at up to 100,000.

It was a far cry from the hundreds of thousands, even millions, of Iranians who turned our for pro-Khomeinin and immediately after the revolution. Throughout Iran, however, today's turnout was estimated to total in the hundreds of thousands.

Even as Khomeini spoke, other elements with in the religious leadership were surrounding a note of discord. The Moslem Repulbican People's Party, established by the relatively liberal Ayatollah Kazem Shariatmadari as a counterweight to Khomeini's Islamic Republican Party, backed dissidents' demands that the draft of Iran's new consitution be presented to an elected consituent assembly.

Evidently fearing such a forum will allow liberals to amend the draft, the Khomeini camp has been pushing for a "nominated" assembly or a "yes-or-no" referendum on the new constitution.

A statement issued by the Shariatmadari group's headquarters in Tabriz said national decisions should be made by council of religious leader instead of just one man - a thinly veiled critcism of Khomeini's domination of the provisional revolutionary government.

But Shariatmadari and two other "grand ayatollahs" joined Khomeini in mourning ceremonies at Qom Theological School, a move interpreted by observers as a gestures of reconciliation. Shariatmadari had been boycotting prayer meetings for several days after he was jostled and heckled by Khomeini followers.

Mourners in Tabriz today carried few posters of Khomeini, but hundreds of Shariatmadari, witnesses said.

In Tehran, however, the mourning demonstration was solidly pro-Khomeini. A huge portrait of the white bearded ayatollah hung from the telecommunications building. Banners and posters supporting him bobbed everywhere in the crowd. Absent, though, were the banners of leftist or liberal groups, who boycotted the rally.

[Radio Tehran said that, firing squads executed six more policemen and an army officer at dawn Wednesday for killing innocent people during the shah's reign, Associated Press reported. The broadcast said six police officers died in the town of Desfur, in Khuzestan province. It said the seventh man put to death was an officer at the Tehran Military College.] CAPTION: Picture 1, Aytollah Ruhollah Khomeini warns his opponents during speech at a rally yesterday in the holy city of Qom. UPI; Picture 2, Armed Iranian women guerrillas keep watch on the speaker's platform at a pro-Khomeini rally in Tehran. AP