Five other defendants were acquitted and will be freed, the court said.
Two other men had their cases transferred to another court. One of the transferred suspects was deemed mentally unstable and the other is under 18 years old.
The court's decision follows a ruling last week that sentenced 10 members of Darfur's most active rebel group to death and acquitted three others.
More than 70 JEM fighters have been sentenced to death for the surprise attack in 2008 - which left 200 people dead - but none of them have faced execution yet.
During the attack, the rebels had driven hundreds of miles across the desert and were only a few kilometres from the presidential palace in Khartoum, when they were stopped by government troops.
On Tuesday, JEM rejected Qatar's efforts to broker peace talks with the Sudanese government.
The head of the rebel group's delegation cited Khartoum's failure to honour a previous deal brokered by Qatar in February that would set up future negotiations.
"We maintain our position to not sit down with the government unless real and clear progress is achieved on the ground, in terms of prisoners, displaced people, and especially after the ouster of humanitarian organisations," Jibril Khalil, a JEM official, said after meeting the Qatari foreign affairs minister.
A spokesman for the rebel movement also cited the Sudanese government's expulsion of 13 foreign relief organisations from Darfur last month, and the death sentences against its members, as reasons why peace talks could not continue.
The United Nations says that 2.7 million people have been forced to flee their homes and up to 300,000 have been killed since ethnic minority rebels began challenging the Arab-dominated Khartoum regime in early 2003.
Khartoum says that only 10,000 have been killed.