The violent beak-up marked a turn in the standoff between the protesters and the military, which removed autocratic President Omar al-Bashir from power in April after a months-long popular uprising against his 30-year rule.
Later he walked out scowling after prosecutors read out the charges he faces - money laundering and the illegal possession of large amounts of foreign currency.
It was to be an acknowledgment of the group's pivotal role in four months of street protests against Mr Al Bashir.
The protest camp was dispersed after talks between the Alliance for Freedom and Change the umbrella protest movement, and a transitional military council collapsed over installing civilian rule.
A top Sudanese general said yesterday that he would execute anyone found responsible for killing protesters after June 3, when security forces moved to break up a sit-in outside the headquarters of the armed forces in Khartoum.
In Khartoum, the strikes in opposition to the 75-12 months-outdated former president triggered scorn and skepticism from critics who dismissed it as a try by Sudan's new navy rulers to deflect consideration from a latest bloody crackdown on protesters, in addition to its reluctance to cede energy to a civilian-led transitional administration.More news: Breaking down the true and false in Trump’s Orlando campaign kickoff speech
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Gen Dagalo has been the most among the generals in his stance towards the protest leaders, questioning the extent of their representation and calling them foreign agents.
Mr Bashir would possibly be wanted by the Global Prison Court (ICC), accused of organising battle crimes and crimes against humanity in Sudan's Darfur situation - expenses he denies.
Prosecutors say a large hoard of foreign currency was found in grain sacks at Mr Bashir's home after he was ousted, bringing to an end almost 30 years in power.
"We are working hard to take those who did this to the gallows", Mohamed Hamdan Dagalo, deputy chief of the ruling military council said on Sunday in a speech broadcast live on state television.
At least 128 people have been killed since the June 3 crackdown, the majority the day the sit-in was cleared, according to doctors linked to the protest movement.
On Friday after a visit to Khartoum, the U.S. assistant secretary of state for Africa, Tibor Nagy, called for a credible and independent investigation into the killings.
"Dagalo's comments were serious indication that the council wouldn't stick to the previous deals despite the Ethiopian mediation", he said.