The thing that changes it from an Equal Protection standpoint is that the vast majority of transgendered people require medical care specific to that condition while that isn't true based upon race, religion, etc. Be it hormone treatment, monitoring of hormone levels or counseling. All the people I know who are transgendered will flat out say that their hormones are a crucial part of their well being and aside from physical changes if they miss a dose their emotional stability and mental clarity take a huge fast hit as well, and that's a legitimate medical issue.
And while not every transgendered person does require that treatment the military has long been allowed to disqualify people based on medical needs or diagnosis broadly even if some percentage of people with the diagnosis would be ok to serve because it's more efficient than going case by case by case to find the exceptions to the rule.
For example- sleep apnea. If you are diagnosed with sleep apnea you can't enlist and if the diagnosis happens after you are in you can't deploy and therefore will in almost all cases be medically separated. The reasoning is that most people with sleep apnea require a CPAP, a CPAP requires electric power, and in a deployed environment they cannot ensure you will have access to both. Now, there are some people with sleep apnea who can get by without a CPAP, but the military isn't going to do a case by case evaluation for new enlistees to spend time figuring it out they just say "no sleep apnea".
What I expect will happen will be something just like that. Or how they handle diabetes now. If your not in already the condition will be a bar to enlisting. If you are in a medical review board will look at your case and apply the same standards used for other medical issues to determine if you are deployable. Or if care needed going forward is consistent with maintaining your ability to deploy. If you are not deployable or will not be for an extended period you will be separated. A few rare cases may be exceptions to the standards found by the board because once you are in they are more willing to try and retain you if your skills are needed- for example I know of only one person retained after he became and insulin dependent diabetic but he was a surgeon so there was a combined factor of him being very expensive to replace and also being only stationed at a hospital even when deployed so a supply of insulin wasn't as big an issue. Even then he had to sign acknowledging that he understood the risks if he was separated from that insulin supply.
It's not fair, for sure. But nothing about military service is. I dealt with having to kick a lot of Soldiers out of the Army Reserve via medical review boards when they developed helath issues. But I always figured that would be the problem here as well and from what I saw and heard they Obama administration had failed to come up with a coherent strategy or policy on handling the medical side of it and had just told the services "figure it out"- and that will leave the door open to change the policy now.
Who knows, maybe in 10-20 years they will develop better ways of hormone treatment like some long term implantable or even synthetic organs. Then that may render the medical side a moot point.
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