Incidentally I will definitely bow to ee on this aspect of employment law. We all have our areas of more and less experience.
If I may weigh in, my 2 cents worth, with a lot of time spent dealing with employers, I am willing to guess it's maybe 25% outright ignorance, and 75% percent "I knew it was shady but I thought I could get away with it." For some reason, these types of issues (misclassifying employees in the name of a little profit) is one of those things like cheating on unemployment benefits that otherwise very nice and outspokenly moral people will do. I don't claim to understand it, but I know many people go into small businesses woefully unaware of their tax liabilities, their responsibilities to employees and how they are supposed to do things.
I also know how in every state, our federal and state departments of labor spend extensive time and money and effort educating employers on the unpleasant realities of tax law, unemployment law, wage and hour, all these issues where fudging isn't legal, no matter how much you'd like it to be. This employer may or may not have been remiss in unemployment tax payments to the state, which is also illegal, and would come back to bite them in back taxes as soon as it gets reported anywhere if they are due. I would suggest that the state Wage and Hour department would be a good place for this employee to start talking.
In my line of work, we had a sort of unofficial perception that for some reason, medical, dental and veterinary offices seemed to be some of the chief offenders in issues of this type, like misclassification of employees. Instead of hiring a competent office manager, they'd try to cut corners. They'd hire their wife, their girlfriend, or their old buddy from college, and go into things wide open and cheating blatantly all the way. And in the meantime be presenting themselves as the most moral people you could dream of, not really considering this type of cheating as anything illegal or immoral.
Yes, in a way they didn't know better, but then if they'd taken the trouble to read all the material they'd been given as soon as they identified themselves as employers, or listened to what they'd been told by professional organizations, or their accountant, or taught in school they would have known better. They just didn't pay a lot of attention to doing it right because they know how they want to do it, how they'd like it to be. And when they're caught or challenged, they howl like mad about the unfairness of the system and the mistreatment of small businesses by our big horrible government.
This gentleman's wife really should have known better than to accept a job under these terms in the first place. She wasn't a contractor, both parties in this pretty much knew that, or could've found out without much trouble.
In employment issues, it is really important to be an "Army of one" and to be alert to any employer misreporting or misconduct. That said, I'd certainly try to work with the employer, talk to authorities about the situation and get this matter dealt with. I wouldn't work any more for them as a misclassified 1099.