No, the correct way to do this is to use the individual's pronouns. Please note that the AP and the NYT have basically adopted the GLAAD style guide on this issue: http://www.glaad.org/reference/transgender

The NYT correctly stated in the parent article, "Ms. Manning was still known as Bradley Manning when she deployed with her unit to Iraq in late 2009." See how that works? She was always a she, even though she was presenting as a man at the time.