Some 5,000 people turned out under a heavy police presence to attend the funerals of the nine men, found guilty of killing Mohamed Taha Mohamed Ahmed in September 2006.
Some in the crowd chanted slogans in support of the Sudan Liberation Movement, a Darfur rebel group which has been fighting the government in the western region of Darfur.
Local radio, citing witnesses and security sources, reported that relatives of the executed men had clashed with police in two places.
Witnesses said a small number of demonstrators destroyed and damaged shops and cars on the way to the funerals.
At the men's trial, the lead police investigator said the defendants had been infuriated by an article in Ahmed's newspaper, al-Wifaq. A defence lawyer said the article played down reports about rape in Darfur and used unflattering language to describe Darfuri women.
The newspaper had also angered Islamists with articles about the Prophet Mohammad and had criticised the ruling National Congress Party of President Omar Hassan al-Bashir.
The human rights group Amnesty International condemned the executions, saying the men were tortured to extract confessions.
"The execution of the nine men is outrageous. They were arbitrarily arrested, tortured and then subjected to an unfair trial," said Tawanda Hondora, Amnesty's Africa Deputy Director.
The government, viewing the killing of the editor and the trial as sensitive matters, initially restricted reporting of the case to state media.