The operation at Islamabad's Lal Masjid has again turned the spotlight on Pakistan's madrassahs, which are accused of links to attacks at home, in neighbouring Afghanistan and as far away as London.
Burqa-clad students from a female Islamic school within the mosque compound and a male seminary in another part of the city initiated the confrontation with the government earlier this year with their freelance anti-vice campaign.
Several male students linked to the mosque were believed to be among more than 53 rebels who were killed when commandos stormed the mosque on Tuesday, security officials said. The organisation that oversees Pakistan's 13,000 registered madrassahs, the Wafaqul Madaris, denies that students are involved in extremist activities.
"Like no human being can survive without water and air, no Muslim society can survive without madrassahs," Mufti Mohammad Zareen Khan, a senior official from the organisation, told AFP. "Madrassahs are not involved in extremism. If teaching the concept of jihad in Islam is viewed as an act of extremism by the West, we do not accept it."
He said that the schools cater to the "poorest of the poorest", providing children with free education, board and lodging, plus tutoring in the tenets of the religion. Yet, only two years ago, President Pervez Musharraf promised a massive crackdown on madrassahs after it emerged that some of the suicide bombers who struck the London transport network on July 7, 2005 had attended them.
At the time he ordered all foreign students to leave Pakistan. Plans to register them all have, however, moved slowly amid resistance by the groups that run the schools. Some 6,000 have not done so. Radical madrassahs, particularly in Pakistan's violent tribal areas bordering Afghanistan, have more recently been accused of training fighters for the Taliban insurgency there.
Multinational forces with around 50,000 troops in Afghanistan, and Afghan President Hamid Karzai, have repeatedly urged Musharraf to tackle the problem of militancy in Pakistan's madrassahs. Many of them were set up, often with US and Saudi funding, as indoctrination and military training sites during the 1979-1989 US-backed guerrilla war against the Soviet occupation in Afghanistan.
The most hard-line schools, particularly near the Afghan border, went on to produce thousands of young recruits for the Taliban, both when they ruled Afghanistan from 1996 to 2001 and then after the regime was ousted by a US-led coalition.
Muttahir Ahmed, Professor of International Relations at Karachi University, said that while Musharraf may have tackled one of the most radical madrassahs, the Red Mosque's Jamia Hafsa girls' school, others would still cause problems.
"Jamia Binoria in Karachi and Jamia Hafsa in Islamabad are mother institutions for the Taliban. The madrassahs will not let him do it again and can come back more strongly," Ahmed said.
And, Musharraf could even face opposition from the more moderate schools. "Muslims should stop paying tax to the government after what they did to the Red Mosque and its madrassah," said Qari Sher Afzal, a senior member of Pakistan's largest alliance of religious parties, the Muttahida Majlis-e-Amal, or United Action Front. "The attack is a death warrant for all madrassahs, and Muslims should not allow such attacks," he said.