Judge Osborne ruled what he described as "political issues" raised as a defence were not a matter for the court.
He told Mr Witherow, president of the organisation under its new name, Sort the System, those matters were "for another domain".
"That is not an inquiry for this court to embark upon."
The Dunedin City Council and STS have been locked in a dispute about the payment of court costs since earlier this year.
In May, the council initiated legal proceedings to recover an $11,060 debt, or force the organisation into liquidation.
The costs followed an unsuccessful court challenge against the council's funding of the Forsyth Barr Stadium.
Council chief executive Jim Harland and STS met earlier this year to discuss payment options, and Mr Witherow said, at the time, he planned to pay, not at the time stipulated by the council, but closer to October's elections.
At the hearing, Judge Osborne said while he appreciated the society had not taken legal advice, Mr Witherow had been told in July, when he gave the court registrar his statement of defence, it was not in a form the court could accept.
The statement included STS' version of negotiations with Mr Harland, with claims the society was "quite able" to pay its debts.
It said there had been an agreement with Mr Harland to complete repayment by December 18, but those negotiations had been set aside for a "steep schedule" of payments the society could not meet.
To close down STS was a "swindle upon the ratepayers, who will be doubly defrauded through paying legal fees merely to ensure no further recovery of debt".
The society had paid $5940 from an initial debt of $15,820; $4740 from a security bond it lodged with the court last year, and $1200 it paid since negotiations with Mr Harland.
Mr Witherow told the court he had had time constraints, and was not a lawyer, but did not see why a "legible document" was not acceptable.
"I'm telling you they were not in the correct form; you insisted in filing it," Judge Osborne responded.
Mr Witherow said he was at the court to represent STS.
"If you say I can't say anything, that's the way it is," he said, prompting a rejoinder from the judge: "I don't know what that's supposed to imply".
Judge Osborne said he was listening to Mr Witherow, but "it's a question of what you want me to do with the document you filed".
The society clearly was insolvent, as it could not pay what was demanded, and from what Mr Witherow said, Mr Harland had not agreed to its payment plan.
"What is it you are saying is your defence?"Mr Witherow said he was asking for the indulgence of the court, that it "simply gives us time to pay".
Judge Osborne ruled the society should be liquidated, and indicated there would be costs to the plaintiff.
In a press release yesterday, Mr Witherow said the organisation was "a little disenchanted with the law".
After the hearing, he said he understood liquidation meant the organisation's assets would be disbursed by the court.
Asked if there were any, he said: "No".
Politically, it could not just start again with a different name, but there was "some fancy footwork" going on to get another organisation started to fill what he said was a vacuum created by the decision.
Mr Harland reiterated his position yesterday, saying he was treating STS as he would any other debtor.
He understood an official would be assigned to look at the organisation's books to see if there were resources to pay, although he did not expect there would be.
