The key way to think of this is that the pronoun is an honorific which always signifies the current state of the individual, and it is not a historical fact. If facts related to the individual's gender at an earlier time are germane, such facts should be explicitly stated rather than overloading the pronoun, which (remember) is simply an honorific which the user has selected.
The question of gender earlier in one's life in most stories is not even relevant and there is really no need to discuss it at all. However, in Manning's case the question of gender does appear to be somewhat relevant, since her motive appears to have included concerns about how the Army treated (or failed to treat) her own gender disorder.
> The question of gender earlier in one's life in most stories is not even relevant and there is really no need to discuss it at all.
Except that gender neutral singular pronouns are not used much in English where they exist (there is a singular they, but it's uncommon it's used). But I think focusing on this is missing the point. Note my reference to Cassius Clay. I'm more interested in that an identifier changes. That the gender specific also changed is just an additional complication, but once the rules on the name are clear, the rules on the pronoun would be obvious, I think.
The question of gender earlier in one's life in most stories is not even relevant and there is really no need to discuss it at all. However, in Manning's case the question of gender does appear to be somewhat relevant, since her motive appears to have included concerns about how the Army treated (or failed to treat) her own gender disorder.