The most accepted usage among those sensitive at all to gender identity (since the person is the same) seems to be to use the current pronouns for all references to the person, even if they are to times before their current gender identity was generally recognized by others (or even formed clearly, though only the former is arguably relevant in this discussion of Manning.)
> At the time of the leaks Chelsea Manning identified as Bradley, a male.
Manning's first discussion with a gender counselor about identifying as a woman was a couple months before her first contact with WikiLeaks; presumably there was some time lapse between recognizing the identity and talking to a counselor. So, from the evidence available, I don't think it's correct that Manning identified as male at the time of the leaks.
> At the time of the leaks Chelsea Manning identified as Bradley, a male.
Manning's first discussion with a gender counselor about identifying as a woman was a couple months before her first contact with WikiLeaks; presumably there was some time lapse between recognizing the identity and talking to a counselor. So, from the evidence available, I don't think it's correct that Manning identified as male at the time of the leaks.