In a note posted on Iranian news websites, Alaei said that he wanted to give a picture of the repressive and dictatorial behavior of the shah, who was ousted from power following the 1979 revolution.
Alaei's op-ed piece has been interpreted -- both by hard-liners inside Iran and also by opponents of the Iranian regime inside and outside the country -- as criticism of some of the decisions made by Iran's Supreme leader Ayatollah Khamenei, including using force against antigovernment protesters in 2009 and denying opposition members the right to protest peacefully.
Some observers had said Alaei was warning Khamenei to learn from his mistakes and not to end up like the shah, who was forced into exile.
Twelve commanders of the IRGC expressed regret over the letter, which they said had brought joy to Iran's enemies. Dozens of hard-liners staged a protest outside Alaei's residence.
Following the criticism and attacks, Alaei wrote that his article had been misinterpreted.
"Unfortunately, some of the domestic media, with their own interpretation, paved the way for foreign media to say whatever they wanted and analyze the article based on their own guesses," he said.
He added that he will continue on the right path of opposing despotism, defending the true nature of the Islamic Revolution, and confronting the dominance of the United States, which he said he has been doing all his life.
He concluded by saying that support for the concept of velayat-e faqih -- the rule of the supreme leader -- preserves Iran from any harm.
One Iranian analyst told Persian Letters that Alaei is trying to lessen the pressure he's been facing over the past days but that he is not backtracking.
"He pays respect to the Islamic Revolution and gives lip service to the velayat-e faqih, but he repeats his point -- albeit softly," the analyst said.
In his article, Alaei names and praises the founder of the Islamic republic, Ayatollah Ruhollah Khomeini, for his guidance and leadership of the revolution but never mentions Khamenei, who succeeded Khomeini.
"That's exactly the irony," the analyst said. "He may be suggesting that Khamenei is not the real follower of Khomeini and his velayat-e faqih. Isn't it what many reformists say? They believe that if Khomeini was alive, things would have been different."
In its January 16 editorial, the ultra-hard-line "Kayhan" daily, which often reflects the views of Khamenei, criticized Alaei's original op-ed piece while expressing hope that his subsequent note is the "first step" in returning from the "deviated path" he has taken.
-- Golnaz Esfandiari