Egypt's military rulers have promised to pardon hundreds of civilians convicted in military courts, amid mounting pressure following the imprisonment of a leading revolutionary activist and the publication of a secret letter from his jail cell.

The damning anti-junta missive from jailed revolutionary Alaa Abd El Fattah was released as draft constitutional principles that could hand unprecedented power to the army were published.

Cairo's ruling generals responded to mounting criticism by announcing plans to free 334 people locked away since the fall of Hosni Mubarak in February.

Abd El Fattah's wife, Manal Hassan, told the Guardian that the military's gesture was a drop in the ocean, given the thousands of Egyptians convicted by military courts. "We're happy for those that will be released but they should never have been there from the beginning, and it does nothing to change the unjust system that put them in jail in the first place," she said.

Abd El Fattah'scousin, Omar Robert Hamilton, a film-maker, said: "Alaa isn't in jail to bargain for specific prisoner releases. He isn't in jail to bargain at all. He's in jail because he won't submit himself to this illegal and unjust tribunal system. So that system has to end, and oversight of the law be returned to the civilian judiciary."

Human rights groups estimate that more than 12,000 civilians have been processed through military tribunals this year, including several protesters, bloggers and journalists who have publicly questioned the army's commitment to democratic reform.

Field Marshal Mohamed Hussein Tantawi, the head of Egypt's Supreme Council of the Armed Forces (Scaf) gave no details of who would be pardoned or when, but said the move was to support "continued communication with the great Egyptian people and the youth of the revolution".

Earlier on Wednesday the gap between Scaf and the "youth of the revolution" was laid bare in Abd El Fattah's letter, which was written covertly inside Bab el-Khalq prison and jointly published by the Egyptian newspaper al-Shorouk and the Guardian.

In it the 29-year-old – who was a political prisoner in 2006 under the Mubarak dictatorship and was re-arrested on Sunday evening – directly accused the junta of being behind the recent bloodshed that left 27 dead at a downtown Cairo protest last month, and suggested that the revolution was being hijacked by the generals.

"I never expected to repeat the experience of five years ago," he wrote. "After a revolution that deposed the tyrant, I go back to his jails?"

He is being held in what he describes as a cockroach-infested 6ft x 12ft cell with eight other men, who Abd El Fattah describes as "poor, helpless, unjustly held – the guilty among them and the innocent".

"I spend my first two days listening to stories of torture at the hands of a police force that insists on not being reformed; that takes out its defeat on the bodies of the poor and the helpless," he continued.

Addressing the killing of Mina Daniel – a Coptic protester who died during the 9 October demonstration but has since been accused, like Abd El Fattah, of helping to instigate the violence, he says: "They [the military] must be the first who murder a man and not only walk in his funeral but spit on his body and accuse it of a crime."

Attempting to communicate with the outside world can be exceptionally risky in Egyptian jails. Last week a prisoner at Cairo's high-security Tora prison died after trying to smuggle a mobile phone SIM card into his cell; witnesses have said he was repeatedly tortured by prison guards who caused internal bleeding by inserting a large water hose into his mouth and anus. Despite the dangers, Abd El Fattah gave permission for his letter to be published.

Manal Hassan, who is heavily pregnant with the couple's first child, visited Abd El Fattah again on Wednesday and told the Guardian that despite terrible conditions, her husband was remaining strong. "He is aware of the huge solidarity campaign that has sprung up to support him, and that has enabled him to stay optimistic and cheerful," she said. "We had a lot of hope for change in Egypt after Mubarak fell, but Scaf is destroying and reversing those hopes day by day."

Several thousand Egyptians marched this week against Abd El Fattah's incarceration, which has been condemned by Amnesty International and labelled "a major setback for the Egyptian revolution" by presidential candidate Abdel Moneim Aboul Fotouh.

In a further indication of the legitimacy crisis engulfing Scaf, civilian political leaders hit out on Wednesday against a new set of "constitutional principles" drafted by the generals and designed to help shape the writing of the country's new constitution following parliamentary elections later this year.

Several party leaders walked out of a meeting with the deputy prime minister Ali al-Selmy to discuss the principles, which are technically non-binding but aim to govern the process and content of the new constitution.

Ahmed Shukry, official spokesman on al-Adl party, reportedly labelled parts of the document "catastrophic", including clauses that would shield the military budget from civilian oversight and allow Scaf to intervene in the process of writing the constitution. Several human rights organisations had already decided to boycott the consultation.