The daily fine was made retroactive to Tuesday.
But Mr. Smith said he knew the commission might impose the daily fines anyway.
The deadline was not met and daily fines of $250 - totalling over $40,000 by the end of 2006 - were levied against the Church.
Work on the building was still at a standstill by March 2009; the daily fines levied by the city then totaled $245,000.
It also requested, under threat of $500 daily fines, that public access be reduced to two and a half days a week.
He also imposed daily fines of $10,000 against the union for disobeying his order to return to work.
And he said he would consider $1,000 daily fines of its leaders, on top of the automatic fines against individual workers.
The commission can impose daily fines of around $5 million on Microsoft if it concludes that the company is not honoring the ruling.
Twitter was given two weeks to comply with the court order before daily fines of €1,000 (about US$1,300) would be assessed.
There are numerous deadlines, with daily fines for missing them ranging from $250 to $10,000.