If you treat a marriage license, not like a government permission slip, but like a contract between two people who wish to be legally recognized as a single unit, then I cannot see the justification for exclusion.
The simple solution to this whole debate over gay marriage is to abolish the marriage license. A license is the government giving permission to do something that would otherwise be illegal (i.e why James Bond had a "license to kill"). If you believe the government should still involve itself in marriage, then the marriage license should be changed to a more complete marriage contract instead of the less complete marriage license. That would allow two unrelated people to sign a contract that legally binds them together as a single family unit. The the only restrictions would be those already in place for contractual agreements, which is simply that the parties involved have to be mentally fit enough to understand the terms of the contract when signing.