A British soldier who refused to return to duty in Afghanistan and went on to speak at anti-war rallies was today sentenced to nine months' detention in a military prison.

A panel of three officers and a judge advocate, Emma Peters, conducting the court martial at Colchester in Essex, also reduced Joe Glenton's rank from lance corporal to private.

He pleaded guilty to going absent without leave in January after the more serious charge of desertion – which carries a maximum jail term of 10 years, rather than two years for awol – was dropped at the last minute.

Glenton, 27, had intended to deny desertion, and his legal team believe the charge was reduced to avoid a potentially embarrassing full trial at which he planned to defend himself on the grounds that the entire Afghan war was illegal under international law.

This would have been particularly sensitive at a time when the status of the Iraq war is being examined by the Chilcot inquiry, to which Gordon Brown is giving evidence today.

Glenton remains a cause celebre for the anti-war movement, writing to Gordon Brown to express his views and claiming support among other troops. A group of Stop the War activists protested outside the army base this morning, with others supporting him in court.

Glenton served in Afghanistan for seven months with the Royal Logistics Corps in 2006. The following June, shortly before he was due to return to the country for a second tour, Glenton fled to Bangkok. He remained in Asia and Australia for just over two years before handing himself in to military authorities in June last year.

The custodial sentence was imposed despite mitigation evidence today that Glenton had been diagnosed with post-traumatic stress disorder which, along with his increasing doubts about the Afghan conflict, meant he did not want to return to the country. Glenton's psychiatric condition had been largely ignored by his commanders, said his defence counsel, Nick Wrack.

The only advice Glenton was given on his return from Afghanistan, Wrack told the hearing, was a speech from a padre who said: "Don't go out and drink too much and beat up your wife." Wrack said Glenton had then faced bullying and intimidation when he tried to tell his sergeant his wider concerns about the conflict.

"When he raised his objections to going back he was called a coward and a malingerer. He is neither of those," Wrack said.

Glenton had never been a pacifist, Wrack explained, and had joined the army in 2004, aged 22, while idealistic and "a bit naive". He had looked forward to going to Afghanistan, where he had been told UK forces were helping the local population.

"Over the course of his seven months [in Afghanistan] … his experiences began to conflict with what he had been told," Wrack said. "More and more he began to see the conflict in Afghanistan was wrong."

Despite these doubts he had worked diligently in Afghanistan, and the court heard testimony from officers who praised Glenton as ambitious, intelligent and a good leader, promoting him from private.

Lars Davidsson, a consultant psychiatrist, testified that he had diagnosed Glenton as suffering from post-traumatic stress disorder. Although he had not served on the front line, Glenton's base in Helmand province came under rocket and mortar attack, and his work preparing coffins for dead soldiers left him with feelings of "guilt and helplessness".

The condition manifested itself in symptoms including nightmares and heavy drinking, Davidsson said. The court martial heard that Glenton had seen an army GP and was due to see a psychiatric nurse before he fled. The decision was not the best in retrospect, but had been motivated by his psychiatric condition, Wrack said.

Glenton returned voluntarily after meeting his now wife, Clare, in Sydney. She wept as Wrack read aloud her letter to the court pleading with them not to jail him so they could restart their lives. She was comforted by Glenton's mother, Sue. Glenton wished to leave the army and had a provisional university place to study international relations, Wrack added.

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