An 84-year-old nun was handed a 35-month jail term on Tuesday for breaking into a US nuclear weapons plant and daubing it with biblical references and human blood. Sister Megan Rice was sentenced alongside two co-defendants, Greg Boertje-Obed, 58, and Michael Walli, 64, who both received 62-month terms.

At an earlier hearing in January, a judge ordered the three Catholic anti-nuclear protesters to pay $53,000 for what the government estimated was damage done to the Y-12 nuclear weapons plant at Oak Ridge, Tennessee, regarded as one of the most secure in the world.

All three defendants were convicted of sabotage after the 2012 break-in, on charges that carried a maximum sentence of up to 30 years. The government had asked for the trio to be given prison sentences of between five and nine years.

In a recent interview with the Guardian from prison, Rice said she hoped US district judge Amul Thapar would seize the opportunity to "take his place in history" and sentence them in a way that would reflect their symbolic, non-violent actions – actions she said were intended to highlight the US stockpile of nuclear weapons they believe is immoral and illegal.

Rice and her co-defendants have been in prison, mostly in Ocilla, Georgia, for nine months, a period of time her lawyers had argued was sufficient punishment for the break-in.

On 28 July 2012, the three activists cut through three fences before reaching a $548m storage bunker. They hung banners, strung up crime-scene tape and hammered off a small chunk of the fortress-like storage facility for uranium material, inside the most secure part of complex. They painted messages such as "The fruit of justice is peace" and splashed small bottles of human blood on the bunker wall.

Although the protesters set off alarms, they were able to spend more than two hours inside the restricted area before they were caught. When security finally arrived, guards found the three activists singing and offering to break bread with them. The protesters reportedly also offered to share a Bible, candles and white roses with the guards.

The Department of Energy's inspector general wrote a scathing report on the security failures that allowed the activists to reach the bunker, and the security contractor was later fired. Some government officials praised the activists for exposing the facility's weaknesses. But prosecutors declined to show leniency, instead pursuing serious felony charges.

The activists' legal team had received hundreds of letters and a 14,000-signature petition pleading for leniency in the case, including from Rice's religious order, the Society of the Holy Child Jesus, which asked for a reduced or suspended sentence given "her age, her health and her ministry". Lawyers for Rice, Boertje-Obed, a Vietnam veteran from Washington DC, and Walli, a painter from Duluth, Minnesota, had also pleaded for leniency.

But the US government argued at the January hearing that they did not accept that they had committed crimes, took no responsibility for them, showed no contrition and then, during the trial, proceeded to argue against the laws they had broken. It has described the three, who have previous convictions related to their protest activities, as "recidivists and habitual offenders".

Jeffery Theodore, the assistant US attorney general for the eastern district of Tennessee, told the court that the three "pretty much celebrated their acts". At the earlier hearing, he described their argument that they were trying to uphold international law as "specious and disingenuous" and said there had been no single case where international law has been seen as justification for breaking US laws.

At the January hearing, four character witnesses for the defendants gave powerful testimony about their strong Christian and pacifist principles, their commitment to helping others, and their dedication to their cause. They, and the scores of supporters crowded into the courtroom, also provided an insight into the close-knit nature of the anti-nuclear faith community.

Mary Evelyn Tucker, director of the Forum on Religion and Ecology at Yale, who has known Rice all her life, compared the nun's use of non-violent protest to the "lineage of transformation" employed by Mahatma Gandhi, Nelson Mandela and Martin Luther King. She said: "To allow Megan to continue the work of her life, the work to alleviate suffering, outside the walls of a prison would be an invaluable gift to the world. To keep her inside, the world would be diminished for lack of her work."

Kathy Boylan, of the Dorothy Day Catholic Worker Community in Washington DC, where Walli is a member, described him as a "quintessential Christian". Under questioning from Theodore, Boylan, a plowshare activist, admitted that, if Walli were to be re-integrated into her community, she would not discourage him from pursuing similar protest action in the future.

• This article was amended on20 February 2014. An earlier version gave Rice's religious order as the Society for the Holy Jesus, rather than the Society of the Holy Child Jesus.