I don't think there should be an issue of using "Bradley" in news reports in the proper context, just so people are aware of who we are talking about. When she was arrested, she was still known as Bradley Manning, and most people probably remember a "Bradley" Manning in the news, but maybe not a Chelsea. So, for example, a news report I think could read as follows without causing offense:
"Chelsea Manning, formerly known as Bradley Manning, had her sentence commuted by President Obama today after...."
I guess I think it is about intent in using the old name. It is just an old name, and using it to simply clarify who we are talking about shouldn't be a problem anymore than a woman who recently got married being referred to as "Mrs. Alice Jones, nee Smith" should. But I can see how deliberately using the old name instead of the new one is indeed very offensive, as it shows a lack of respect for the choices a grown adult makes. But I am a straight white male, who doesn't really know anybody in the trans community. If I am off-base and any trans person or advocate is reading and wants to fill me in on how the community really feels about this, I am all ears.
In any case, I really don't understand or agree with this commutation. Snowden has a better case if you ask me, and I wouldn't likely support that one either. Manning leaked a tremendous amount of classified info for no apparent purpose. The exposure of the journalist's deaths was only a small part of what was leaked. Manning, in my opinion, is someone who simply should not have had a security clearance.