That was why DOMA was passed. Social Security, Medicare, federal pensions, etc. would all be affected if same-sex marriage would be approved by the USG.
The reason for the problem is that the Federal Gov has exceded its constitutional authority, and the federal income tax.
I would prefer that the states had the choice to do what they want, and then observe the results upon each state. The only federal issue would then be gays in the military.