Exactly what Bush said is that this is a state issue (marriage licenses are issued by the state, after all) unless they come down on the side of homosexual marriage, then he'll make it the FedGov's business to clarify the definition of a marriage. Sounds clear enough to me, unless you are one of those that thinks the FedGov ought to interfere in state's rights.
civil union is an attempt to create a "marriage" by another name. Bush is ducking the issue.