Given their "fuck it" roots, I'm not actually sure how much of a shield they provided between you and Microsoft's Accounts Payable. I bet they paid you every week like most of these staffing firms no matter how fast or slow Microsoft felt like paying its invoices. I'm also pretty sure they provided you with equipment (though how that works if you are also a 1099... I'm not sure).
What a lot of people who haven't done true 1099 work don't realize is... people and companies can be incredibly slow paying you. And as a 1099 you are your own collection agency so it's upon you to hassle them into paying you.
What I'm saying is... if there is a will there is a way. I bet there is more than a few Microsoft contractors who act like their own agency. It's probably a lot of paperwork, and I have no clue if it is worth it.