I'm sorry, I have not consulted with any Houston CPA concerning this situation. When choosing a CPA I would ask them if they are familiar with "employees of a foreign government" and "green card holder". Also ask them if they are qualified to interpret the tax treaty for your spouse's country. Please prepare by reading the official IRS explanation by searching "IRS employees of a foreign government", and click on the IRS link. I think it is fairly easy to understand.
The more difficult question is "why is your spouse not allowed to voluntarily pay self-employment tax (for social security, etc.), when they work for a foreign government, but they get the tax automatically deducted when they work for any other firm?". I suspect few can answer that, but it just points out one of the many long-term disadvantages (not getting work credit for their own social security account) for a green card holder working for a foreign government...
