When you file a joint tax return, all of the income  from both spouses is combined.  The credits and deductions are shared, the dependents are claimed by both people, etc.  It is not broken down by "his" and "hers".  It is not clear why your spouse's employer would reimburse her for her portion of income tax paid.  Certainly the employer can look at her earnings and see how much they paid her and how much tax was withheld from her pay.  

Her income is from United Nations and comes out side of USA. They have a policy of reimburse the tax paid on income earned. Turbotax took all the correct information and recommended filing jointly. If I can give a statement to the reimbursing authority that out of total income filed jointly x amount is tax for the part of her income. They don't deduct any income for the USA at all.