Generally, it is better for a couple to file a joint tax return.  The fact that you qualify for the foreign earned income exclusion has no bearing on the filing status you choose.  If you file separately you lose the opportunity to claim some tax credits/deductions that would be available to you if you filed a joint return.

This link to the Turbotax help page Should You and Your Spouse File Taxes Jointly or Separately? provides additional information that you may find useful.