Pvt. Manning's transgender defense didn't hurt the transgender community in that it was a ploy to avoid the death penalty as a traitor to his country. Manning's plea may have been truthful, but the way he used it to defend against treason was ludicrous. Having transgender issues is no excuse to betray your country so heinously that it put people's lives in danger. Manning knew precisely what he was doing and why--Julian Assange found a witting accomplice and took advantage of a desperate individual who was depressed and needed money. Manning's basic training should have kicked in sometime during his conversations with WikiLeaks.
Althought Pvt. Manning's transgender defense did raise a lot of questions that may have negatively impacted the transgender community, it's still not something that would hurt them in the long run. This event gave the community much more disclosure, and forced the relevant parties to consider the situation in more scrutiny, which is something that thus far has not had much exposure.