Maxine Carr has been "vilified" and cast alongside Moors murderer Myra Hindley, the Soham trial has heard.
Holly Wells and Jessica Chapman died in August 2002
Michael Hubbard QC said there was an "incalculably evil" side to Ian Huntley of which his client had been unaware.
Ms Carr denies conspiring to pervert the course of justice and two counts of assisting an offender.
Mr Huntley denies murdering Holly Wells and Jessica Chapman, although his lawyer has said there may be evidence to support a charge of manslaughter.
Summing up Mr Justice Moses told jurors to judge the case on the evidence and not to be influenced by the emotion it provoked.
He said they knew that while Holly and Jessica's families were searching for the 10-year-old girls, Mr Huntley was disposing of the bodies.
But it did not prove he murdered them, the judge said.
In his closing speech for Ms Carr's defence, Mr Hubbard said his client had admitted telling lies but she had believed Mr Huntley to be innocent of killing the girls.
She was just trying to protect him from revelations about a previous allegation of rape against him, the trial heard.
She could see something had occurred in the Soham house she shared with Mr Huntley on returning from visiting her mother in Grimsby, said Mr Hubbard.
But Mr Huntley told her the bath had cracked and she had believed him, the court heard.
Mr Hubbard said it was "a bit rich" for prosecutors to claim Ms Carr should have worked out the whole story on her return to Soham, when they had had 16 months and still did not have all the answers.
Her surprised reaction in police interviews and anguish during calls to Mr Huntley's mother showed she did not know Mr Huntley had killed the girls, Mr Hubbard said.
And the prosecution claim that the pair had agreed an alibi on Monday 5 August - the day after the girls' disappearance - was unlikely, he said, because she did not return from Grimsby until the Tuesday.
There was an "incalculably evil" side to Mr Huntley that Ms Carr had not known about and Mr Hubbard told the jury he "didn't rely on a word Ian Huntley said".
It was Mr Huntley, not Ms Carr, who came up with the alibi, he said.
Mr Hubbard also read out a leaving card given to Ms Carr, a former teaching assistant, by Holly in which fellow pupils said they would miss her a lot.
Mr Hubbard said: "These two little girls were very special to Maxine Carr and she to them.
Mr Hubbard said his client had just wanted to "stand by her man"
"And we suggest it is almost preposterous to suggest that she would conceal what Huntley did, having worked out that he had murdered or in some other way
unlawfully killed those girls."
Holly and Jessica disappeared from the Cambridgeshire town on 4 August 2002.
Their bodies were found two weeks later, in an isolated area near the RAF Lakenheath airbase in Suffolk.
Mr Huntley has admitted dumping and burning the girls' bodies.
He told the trial Holly died accidentally, after falling into his bath as he helped her with a nosebleed.
But he admitted killing Jessica by putting his hand over her mouth to stop her screaming.
And he said he had told lies to police to cover his tracks.
In his closing speech on Wednesday, prosecutor Richard Latham QC said "the whole business in the house was motivated by something sexual" that had gone wrong, though there was no evidence of this, Mr Huntley's lawyer said.
The jury will be sent out to consider its verdict on Friday.