As you are filing using Married Filing Jointly status, it does not matter that the home mortgage and insurance are only in your wife's name. And, in many cases, there would be no issue with you and your wife taking deductions for two separate offices in the same home. You would simply file 2 copies of Form 8829, separately computing your respective expenses.

From what you have described in your question, there seems to be no question that you can take your expenses related to the LLC office. I am more concerned about your wife's use of a home office for her work as a "telecommuting intern for a church." The question does not make clear whether she is compensated for this work. This could present a problem, as some home office expenses are limited by the income derived from the use. Further, reviewing the qualifying factors listed below, it should be noted that the deduction is allowed only for expenses incurred in relation to a trade or business. It is doubtful that a church internship would qualify, as there is no profit motive.

To qualify to deduct expenses for business use of your home, you must use part of your home:

• Exclusively and regularly as your principal place of business;
• Exclusively and regularly as a place where you meet or deal with patients, clients, or customers in the normal course of your trade or business;
• In the case of a separate structure which is not attached to your home, in connection with your trade or business;
• On a regular basis for certain storage use;
• For rental use; or
• As a daycare facility.
• Additionally, as an employee, your business use must be for the convenience of your employer.

For more information, please see IRS Pub. 587 Business Use of Your Home.