On Thursday in a Boston court, a 29-year-old Muslim student faces being sentenced to life behind bars in a case that civil liberties groups raises profound questions for freedom of speech in America.

Tarek Mehanna, a bearded Islamist with fundamentalist beliefs, was convicted last year for conspiring to provide support to terrorists by downloading jihadi videos from the internet and translating Islamist documents that he found online.

Prosecutors portrayed Mehanna as a dedicated radical who tried, and failed, to get terrorist training in Yemen in 2004 and then devoted himself to promoting and spreading the violent views of radical Islam in America. Defence lawyers had insisted that Mehanna's trip to Yemen was to find a religious school and that his radicalism has been greatly overstated. They say he was a family man, angry at American foreign policy, who considered himself an outspoken Islamic intellectual and saw the west's treatment of Muslims as wrong.

However, regardless of which version of Mehanna's beliefs was the truth, civil liberties groups say the Mehanna case is a huge setback to America's freedom of speech and that he was essentially prosecuted for "thought crimes" that should be constitutionally protected by the First Amendment. "It is thought crime. We should be very concerned about this," said Steve Downs, a New York state lawyer who works with various groups examining legal cases brought against Muslims in the decade since September 11.

The American Civil Liberties Union (ACLU) tried to file a brief in support of Mehanna during his prosecution but was refused the opportunity by the presiding judge. The ACLU had argued that Mehanna had consumed information freely available on the web and that his freedom of speech was of paramount importance, even if the material was offensive, anti-American or pro-violence. "This is a big case. Weakening the First Amendment is a slippery slope. Certain federal judges seem to ignore it at will," said Nancy Murray, a director at the Massachusetts branch of the ACLU.

Some observers believe that radical Muslims get different treatment to other extremist groups. Mehanna was convicted of supporting terrorism despite there being no proven active link between him and any terrorist or terrorist organisation, and his activities appeared to consist of spreading easily available material he found on the internet. There is no evidence he actively plotted to take any terrorist action in the US, but he now faces a possible life sentence in jail.

That treatment has been contrasted with the collapse in March of a prosecution against a far-right militia in Michigan that called itself the Hutaree. After a long undercover FBI investigation, seven members of the group were charged with stockpiling weapons and plotting violence . One Hutaree member was recorded talking about killing police officers and the need to go to war against the US government.

FBI agents seized guns, ammunition, gas masks, swords and instructions on how to make grenades and ingredients for explosives. However, a judge dismissed a terrorist conspiracy case on free speech grounds. In the end just two members of the militia pleaded guilty the minor weapons charges. "That is an incredible contrast to what we saw with Tarek Mehanna's case," said Murray.

There is also another twist in the case. Mehanna has said that he was only prosecuted after he refused to become an FBI informant. He said he was approached by FBI agents in 2008 as he was about to take up a job in Saudi Arabia and told he would be prosecuted for his activities unless he agreed to become an informant.

"They [said] wanted to file terrorism charges against me, and that, 'We could either handle this the easy way or the hard way.' I was told to get a lawyer, and he would explain what the 'easy way' was. … Here I am today, having chosen 'the hard way'," Mehanna said in a statement on a website in support of his case.

The FBI has come under intense criticism in recent years for its use of confidential informants among American Muslim communities. It has been accused of trawling entire Muslim communities in nonspecific attempts to secure information on Muslim figures. Former FBI informant Craig Monteilh, who has now joined an ACLU suit against the FBI, earlier this year described to The Guardian how he spent a year undercover in southern California collecting personal information on prominent Muslims, often with a view to entrap then into becoming informants.

At the same time, the New York police department has been hit by a storm of protest from Muslim communities after revelations of a massive blanket spying operation in New York and nearby cities. Downs said Mehanna was simply being prosecuted for refusing to help the FBI. "This is a pattern we have seen before, when the FBI is trying to pressure people into becoming informants and when they don't, they go after them for free speech. Tarek Mehanna's is a classic case," he said.

Defence lawyers have asked for Mehanna to get around six years in prison, while prosecutors were set to file their recommendations later on Tuesday though sentencing guidelines include the option of a life sentence. In a letter to the court with the defence filing, Mehanna asked the judge to consider that he was arrested in 2008 at Logan Airport just as he was about to leave for a job in a diabetes clinic in Saudi Arabia. "I would be making a living alleviating the suffering of others," he wrote.

His lawyers pointed out: "There was no evidence that Mehanna's actions actually threatened United States security interests. There was no evidence that Mehanna provided any tangible material support such as funds or weapons to terrorist activity or to al-Qaida," they said in a statement.