Well, it will still be the case that the 1099-K has your spouse's SSN on it, but the schedule C for self-employment will have your SSN on it, even though they are part of one overall tax return. The IRS may still send a letter, but it will be very easy to answer it.
Turbotax may also get confused when you enter the 1099-K, it may try and create a business for your spouse. You may need to use your SSN when entering the form in the program. I haven't actually tested this, though.
