If a newspaper said "Bradley Manning met with her lawyers today..."
The english language uses gendered pronouns to refer to human beings. He. She. His. Her.
We more progressively minded folks believe that gender identity is subjective.
If you meet someone who you assume is a man and she corrects you it would be very rude to persist in calling her a man, or get into an argument about what being a man means to you. Her identity. Her call.
Similarly, if you thought her name was David and she corrected you with, "I prefer to be called Sally," it would be quite rude to persist in calling her David.
When, however, somebody is a public figure famous for, among other things, standing trial for some crimes, the person's legal name is a meaningful journalistic identifier.
Nobody named Chelsea Manning has leaked anything or been convicted of anything, and if Obama pardoned Chelsea Manning the pardon would be defective.
We use the name Chelsea Manning as a show of solidarity and respect for trans people, and that is fine and good. But referring to a person by their current legal name is never going to be entirely and unambiguously wrong in all contexts, and in some contexts makes a lot of legal and journalistic sense, particularly when somebody is already famous.
Though we have names associated more with males or females, a name is not a statement of gender. In English, he or she is, however, a statement of gender.
If I knew Chelsea Manning I would call her Chelsea. That's basic. And as a show of solidarity with someone I do not actually know, I am using Chelsea here.
But if a newspaper story tomorrow says, "Bradley Manning met with her lawyers today..." I would feel that the paper was making a good faith effort to acknowledge Manning's subjective gender-identification ("her"
while using the most useful objective identifier of the individual being discussed, which is the name by which she is best known.
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That's me looking on the bright side. 