Yes that makes her self-employed.
Although it may be news to you that you “have a business” (and most of the other people who get their first 1099-MISC); The IRS considers anything in box 7 of 1099-MISC to be self employment income. Enter the 1099-Misc income, at Other Common income / income from a 1099-MISC . TurboTax (TT) will complete Schedule C or C-EZ for you and allow you to deduct any expenses associated with this income. You'll also have to pay self employment tax (social security & Medicare) on any profits greater than $400. These types of payments are frequently done this way. Your "employer" is not the only one.
The office is still her work place, so the mileage is not deductible, as it is considered commuting, which is not deductible even for the self employed.
Filing as self employed is the best way to handle this.
That said, there is a way to contest the “employer’s” classification of you as a contract employee. That is to pay your share of the Social security tax on form 8919 .In TurboTax, type> form 8919 with 1099-misc income <in the search box. After you enter your 1099-Misc, select that you got the 1099-Misc for another reason. Then select "My employer reported this extra money on a 1099-MISC but it should have been reported on a W-2" from the drop down list.
You also have to submit form SS-8 and the IRS will determine whether you or the employer pays the employer portion of the SS tax. You will probably also upset your employer, because the IRS may contact him about whether or not he properly paid wages.
Form SS-8 is not in TT but is here ===>>> http://www.irs.gov/pub/irs-pdf/fss8.pdf
See this IRS site ===>>> http://www.irs.gov/taxtopics/tc762.html
