He indicated he had continuing doubts about the Kalispell woman's honesty and said he was "waiting for Ms. Graham to say she was sorry for killing Cody," KGVO-AM reported.
"There's only one person in this room that knows what happened, and I don't think she's been entirely truthful about what happened," Molloy said.
Graham was sentenced to 30 years and five months in prison without the possibility of parole and ordered to pay $16,910 in restitution.
She will be subject to five years of court supervision upon her release.
Prosecutors had recommended a prison term of 50 years to life. They said Graham lured Johnson to the top of a 300-foot cliff in Glacier park on July 7 and pushed him over, then lied repeatedly to investigators in an attempt to cover up the crime.
Outside the courthouse, Johnson's mother, Sherry Johnson, said she felt she could now go on with her life.
"I do feel that I can move forward with this, yes," she said.
Sherry Johnson's sister-in-law, Celeste Watson, said after the sentencing that the family still doesn't know the truth about what happened.
"But we have to accept what went on here today and move forward," Watson said, according to the Missoulian.
In December, as the case was being heard by a jury, Graham dropped her claims of innocence and pleaded guilty to second-degree murder just before closing arguments in the trial.
Prosecutors in return dropped a first-degree murder charge and a count of making a false statement.
Before sentencing, Graham addressed the judge and assembled friends and family members. She claimed to still love Johnson and apologized to Sherry Johnson for the pain she caused.
"It was a moment of complete shock and panic," Graham said of the events surrounding Johnson's death. "I have no other explanation."
Federal prosecutors painted a more sinister image of the defendant.
They said she drove away from the murder scene without checking to see if Johnson survived the fall. And the absence of any drugs or alcohol in the case meant the defendant "was thinking very clearly," Assistant U.S. Attorney Kris Mclean said.
In the days leading up to her sentencing, her attorneys sought to withdraw Graham's guilty plea after prosecutors recommended up to life in prison.
They described their client's actions as "extremely reckless but unintentional" and argued that a 10-year sentence was appropriate. They also portrayed her lies to investigators as "distorted statements" that Graham later sought to clarify because she could not bear the burden of her guilt.
"Embedded within her false narrative were pieces of the truth that the defendant would ultimately reveal (to law enforcement) in pursuit of catharsis," her attorney's wrote in documents submitted to the court earlier this month.
Before he accepted her plea, the judge asked Graham to tell him what happened.
Graham said she wanted to confront her husband about her marriage doubts but did not know how he would take it. She said the couple climbed down a treacherous slope below a popular spot in the park called The Loop and spoke on a narrow ledge, hundreds of feet above a ravine.
She told Johnson she was unhappy, they argued, and at one point, she said, he grabbed her by the arm, and she thought he was going to pull her.
She told the judge she got angry at Johnson, brushed his hand away, then pushed him, with one hand on his arm and one on his back.
"I wasn't thinking about where we were. ... I just pushed," Graham said.
Graham initially told investigators that Johnson left their house on July 7 with unknown friends. But Johnson's friends testified they were suspicious of the story and suspected Graham played a role in his disappearance. Graham showed police a fabricated email — purportedly from a friend of Johnson — that said Johnson was dead and to call off the search.
Ultimately, Graham acknowledged she was with Johnson on the cliff after investigators confronted her with a security camera photo of the couple entering the park.
Prosecutors presented dozens of text messages between Graham and a friend from church that documented how Graham's nervous excitement at the prospect of the wedding turned into despair over the week that followed.
Johnson was reported missing on July 8 when he failed to show up for work. His body was found three days later when Graham led a group of searchers to where she'd pushed him off the cliff.