Well, the way I see it, the new institution of the gay civil union will not be as immediately recognized in the society. If it does not exist in a state, then what will that state's Supreme Court have to go on?
For example, prositution is legal in parts of Nevada. If I pay for "services" in a licensed establishment (not gonna happen, I have no desire for either that, or the wrath of Mrs. Hunter112!), I may well have rights to sue for nonperformance of the contract. I cannot take my claim to another state's court, even if there is a possible otherwise valid reason to do so (such as paying with a credit card that is to be interpreted as being subject to the laws of a state other than Nevada), they will toss it out, based on the fact that prostitution is not legal in the other state. A court outside of Nevada will not enforce an agreement to trade money for prostitution services.
Now, a marriage certificate, on the other hand, has application in each of the fifty states, they all have marriage laws. A case in my state over a credit card dispute concerning provision of dental services in Nevada, if the court has jurisdiction because of the credit card agreement, will be heard and judged on its merits.
Besides all of the above analysis, I sincerely doubt that a Federal Marriage Amendment could pass both houses of Congress by the enormous majorities required, and further, to be approved by three quarters of the states. Even if it did, it would not stop gay marriage or civil union in the states that have it, it would just stop official recognition of these relationships in the states that had not. Private recognition would still go on, maybe even faster. Recall how donations to the Boy Scouts dropped off, even after the Supreme Court reaffirmed their policies regarding gays. Backlash goes both ways.