Williamson, flanked by family members, today presented a cheque for $6,000 to the court, which is likely to be distributed among "three named charities."
And Judge David Saunders indicated that he would not be jailed for his crimes.
The judge said: "He's not someone who needs to be detained in full-time custody. Given he's paid reparation, I'd far rather he was remanded in the community."
The court earlier heard that on April 15 2008, Williamson transferred $1,000 from the charities' bank account to his own.
He then transferred $1,000 on five more occasions over the next few months.
When the transactions were uncovered, Williamson told police he believed he was entitled to the money and used part of it to pay electricity bills.
Today the court was told that Williamson "genuinely believed" he was entitled to the money.
In July this year, The Hope for Children Foundation, the Disabled Children's Trust and Williamson as their sole trustee, were banned from charity work for three years by the Charities Commission.