Simply put: nobody knows in most cases if such a marriage would withstand legal challenge.
The way I read DOMA, such a marriage would be invalid (in places where DOMA's marriage definition still stands) *IF* the Feds decided, FOR THE PURPOSE OF MARRIAGE, you both were the same sex (they could make a different decision about sex for purpose of marriage than, for instance, for social security - there is no requirement for them to be consistent, although I suspect courts would usually strive for consistency). I don't think there has been any case law regarding that (and certainly no statute law), although I suspect if they consider you the same sex in other matters, that could be used against you. If they don't think you are the same sex (in otherwords, don't recognize the transition), you are safe. That applies to federal things, like federal taxes, immigration, federal government benefits, etc. I wouldn't be surprised if the IRS uses your sex that they could get from SSA, so taxes could be an issue).
If DOMA is struck down, I don't know if the feds would use the fact that you were legally married at time of marriage or not. It's a gray area. If they don't, then they would likely use either the definition of marriage where you currently live or the definition of marriage where you got married. One or the other would be used, and that place would need to recognize the marriage for the feds to recognize it.
State benefits and responsibilities, for things like most inheritance, state taxes, work benefits (non-military), etc, would be decided, most likely, by the state you live in. For most states, there is no definition of male or female in case law for marriage (and none in statute law). They have identification requirements for getting licenses, yes, but a driver's license and/or birth certificate doesn't necessarily prove sex even for the purpose of marriage when either can be used to get a license (in other words, someone can present birth certificates with the right sex on them and not legally be able to enter into marriage with a partner with documents of the opposite sex, IF the state decides that they don't recognize the sex change as legitimate - and some don't).
So, at that point, it's up to case law. Either past cases (I don't know of any regarding people who married as opposite sex and then one transitioned) or whatever the random judge hearing the case decides. Certainly if you expect the government to recognize the new sex, it's not likely they will do so only for every area of life except marriage. So if they have law against recognition of same-sex marriage, then likely your marriage wouldn't be valid. On the other hand, if you live in one of the states that has decided sex is immutable from birth for purposes of marriage, you are fine.
Obviously if the state recognizes same sex marriage, you should be fine at the state level (and later the federal level when DOMA goes away).
The basic result of this: your marriage is not safe. No marriage where one partner transitioned is safe throughout the USA today. Anyone that tells you any differently is giving you bad advise. Your marriage *MIGHT* hold up in court if challenged, but nobody knows for most jurisdictions (that said, it would likely be fine in the most anti-trans jurisdictions, where there is anti-trans law that denies recognition of sex change for purposes of marriage, ironically enough).
The only reasonable way out of this legal mess for all of us is to legalize same sex marriage, making sex of each partner irrelevant to the state. For your marriage, that makes a ton of sense just because that would fully recognize what the marriage will be - a same sex marriage. But even for people like my wife and I (a heterosexual marriage), we need such laws to have a secure marriage everywhere in the country.
