Surprised that she can't reassign her "pay to" to a payroll processing company to manage estimated payments as well as local taxes etc. I guess that's what I was asking at the top...
As was mentioned earlier in this thread, she cannot reassign her pay to a payroll company because she is not on anyone's payroll. She is self-employed. e.g., she is running her own business, selling her consulting services to other companies who pay a purchase price to her for the services. This is very different than a salary. She is getting business revenue, from which there are all sorts of business deductions that are not applicable to W-2 salary employees.
As others have mentioned, she may want to set up a corporate shell for her business. The fees paid by her client companies would go to her corporation. And then her corporation can pay her a salary. Alternatively, you might find it easier to hire an accountant to handle all the self-employment taxes she needs to pay.
HOWEVER, I sense from your comments that neither you nor your wife consider her to be an independent contractor, running her own business, selling consulting services to client companies. I sense that you view her role as an employee of the company, who should be paid as a W-2 employee of the company (or W-2 employee of a temporary staffing firm).
If her job is a routine office job, where she is taking day-to-day direction from a supervisor, she may very well be improperly classified. However, if she is a professional (such as a doctor, engineer, or writer) brought in to provide specialized services mostly under her own direction, she may be classified properly.
If she is classified improperly, you may want to talk to an employment attorney to find out your options. But be aware that the company she is working for may be intentionally misclassifying her. If she pushes too hard, she may find her job eliminated, restructured (possibly with a reduction of hours/compensation), or they may move her from 1099 status to a W-2 temporary staffing firm (who will take a significant portion of her compensation, but possibly also offer benefit like health insurance, sick pay, and vacation time).
This is probably way too complicated to address on an internet message board. Your best bet is to talk to an accountant or employment attorney.