You need to check with a student loan expert at the department of education or maybe a consultant somewhere. That's not really a tax question.
I have seen and handled many questions from student loan borrowers in repayment who are planning to file MFS in order to get lower IBR payments. This may have advantages on the student loan side, but may cost a significant amount of money on the tax side. Generally, if you are in IBR for 20 or 25 years, and make on time payments for the entire period, you may qualify for loan forgiveness. But you could be losing thousands of dollars each year on your taxes, especially once you have kids. And the forgiven loan balance (when that eventually happens) is taxable income. I have a feeling that filing MFS to get lower IBR payments is almost always a net loser. But your experience may be different.
I did a short search and I don't see a provision to file a joint return but also exclude your spouse's income from IBR, but you should ask an expert to be sure.
http://www.nolo.com/legal-encyclopedia/tax-filing-status-student-loan-payments.html
