first note that MFS is generally the worst filing status for a married couple. there are rare exceptions. as to your question. A married couple can choose to file using the Married Filing Separately (MFS) status even if they are subject to IRS Notice 2014-7. Notice 2014-7 primarily addresses the tax treatment of certain Medicaid waiver payments, not a couple's federal filing status.
there is no quick correct answer as to what filing status is best. to find the lowest tax you may have to do 3 returns. 1 each MFS and a joint return.
