The public display of divisions and bitter exchanges in the press hurt a movement that presents itself as having clear-cut, divinely dictated answers to the country's problems.
"This is the end of the religious utopia," wrote Khalil Anani, scholar in Islamic movements in the Al-Hayat newspaper. "Mixing ... between political and religious activity is a ticking bomb inside the Islamic currents."
Kamal Habib, an Islamist thinker, said the image of the clerics "has been harmed."
"Clerics should leave politics and let the party work independently from them," he told The Associated Press.
The Al-Nour Party's pragmatists don't necessarily hold more moderate views than its pro-cleric camp. Instead, the dispute centers more on issues of personal power and how much a party trying to navigate Egypt's new political system must adhere to the clerics' strict lines. The party has already repeatedly wrestled with that question.
Unlike the 86-year-old Brotherhood, which is highly disciplined and deeply versed in politics, the Salafi movement is more of an umbrella for various schools that differ in their views, spiritual leaders and methods. For nearly three decades, the Salafi school shunned politics, spreading its message through mosques, charity, and TV stations. It was not targeted in security crackdowns under Mubarak since it posed no political challenge to the ruling regime, unlike the Brotherhood and violent jihadist groups, some of which were offshoots of the Salafis.
But another result is that it is less cohesive than the Brotherhood, clumsier with politics and more vulnerable to splits.
During this year's presidential campaign, many young Salafis defied the party by backing the candidacy of Hazem Salah Abu-Ismail, a firebrand cleric who mixed Salafi and revolutionary ideas but who was not welcomed by Al-Nour's clerics. In the end, Abu-Ismail had to drop out of the race.
The party was further split over which of the two main Islamist candidates to back — Morsi of the Brotherhood or the more liberal Abdel-Moneim Aboul Fotouh, who defected from the Brotherhood. Al-Nour backed Aboul Fotouh out of fear of Brotherhood domination. The elders of the Salafi Call, however, shunned him because of his moderate views and close ties with secularists.
Though both are Islamist movements, opposition to the Brotherhood runs deep among many Salafis, who fear the more organized group will overwhelm them and who say the Brotherhood is too willing to compromise in pursuit of an Islamic state.
Sheik Borhami frequently lashes out at the Brotherhood, warning in one sermon, "If they get empowered, they will curb Salafism, no doubt." He went so far as to meet secretly with Morsi's opponent in the run-off presidential election, Ahmed Shafiq, who was Mubarak's last prime minister — embarrassing Al-Nour when word of their talks leaked.
Another top Salafi cleric Abu Ishaq al-Hawani denounced the Brotherhood's outreach to Christians, who Salafis often say are trying to wreck Egypt's Islamic character. "This is total loss," he said of past meetings between Brotherhood leaders and the Coptic Christian pope.
In contrast, their rival in the Al-Nour Party, Abdel-Ghafour, has become one of Morsi's advisers in a sign of cooperation with the Brotherhood.
"It's politics killing even the most rigid and stubborn ideology," wrote Ashraf el-Sherif, a scholar in Islamist movement studies in an article in April, predicting the collapse of Al-Nour.