I agree with the overall sentiment, but your numbers are not quite correct.
The article in the San Jose Mercury News says that the company had to pay the difference to the California minimum wage, $40,156 in total, plus a fine of $3,500.
So this time, they had in effect to pay the minimum wage, plus $3,500, plus some bureaucratic hassle to deal with the affair. Lets call it a loss of $4000 compared to doing things the lawful way. Had they not been caught, they would have saved $40,156 compared to doing things the lawful way.
That makes it mighty attractive to do it the illegal way at least until the first fine, even if there is an escalating penalty for repeat offenders. I think the penalties need to be much bigger for first offenders, and escalate from that.