The military has often led the country in issues of civil rights. As commander in chief, you are in the unique position of being able to mandate that all legal partners of gay/lesbian service men and women are granted full and complete rights, privileges and benefits afforded family members of heterosexual service members.
Just as the military allows doctors licensed in any state to practice on any federal military base (provided correct credentials are presented), regardless of what state the base exists in, the military could honor civil unions and marriages from any state, regardless the state of the base the couple/family are stationed on.
Repeal of DADT was a step in the right direction! But our gay/lesbian service men and women deserve equality for their service, not small steps.