| The best solution is to issue a 1099-Misc in the name of her business, assuming of course she is conducting a business as either an LLC or as a DBA. This should suffice! Report the amount paid to your spouse on the 1099-Misc and then send a Red copy of the Form 1096 Annual Transmittal Form along with a Red copy of the 1099-Misc to the IRS.
Legally speaking you can still file a joint return as well even if your business issued a 1099-Misc to your spouse's business. It happens all the time! | 
