"Here the allegations are someone has stolen from a children's charity," he said, but urged the jury to put any emotions the allegation might inspire aside to consider the evidence.
Judge Thomas said there was a dispute over the funds between Kidscan chief executive Julie Chapman and Ms Jones, who had both testified, which centred on the number of days over which she was employed and whether the extra holiday payment was deliberate.
The defence had argued Ms Jones was "paying the price" for standing up to Ms Chapman's treatment of staff, including assisting others who had worked at Kidscan with employment action against the charity.
The court had also heard Ms Chapman had gone "high up in the police" with concerns about Ms Jones - and spoken to her new employer about the allegations against her.
The Crown said claims of a "vendetta" were a "smokescreen".
Ms Jones and supporters sobbed as the unanimous verdict was given.
The charity was started in 2005 to raise money for disadvantaged children. It now supports children in more than 400 low-decile schools and has grown rapidly. Its annual revenue went from $3.8 million in 2011 to $7 million in 2013.
The Herald has learned of more than a dozen staff who had left the charity in the past two years, including some who lodged cases with the Employment Relations Authority.
Ms Chapman, in a written statement, said police made the decision to prosecute and there was no influence from KidsCan.
"We are disappointed with the decision of the court but it would be inappropriate to comment further," she said.
Questions over how much money the charity spent on legal bills went unanswered while Ms Chapman said "privacy reasons" meant she could not comment on any other employment matters.
A police spokesman said Ms Chapman had called Superintendent Sandra Manderson for "advice", having previously met the high-ranking officer at a social event.
"As is standard practice, Superintendent Manderson referred her directly to the appropriate police district for follow-up."
Ms Jones remained as a board of trustees member at Dairy Flat School over the duration of the case, with the board saying it would "fully support her in all respects".
Martin Bradshaw, chairman of the Dairy Flat School board of trustees, said: "We are extremely pleased with the outcome of this case and the two not guilty verdicts."
