I think the bigger issue was with allowing him to retain access to classified data while obviously disgruntled and having issues with his chain of command. His unit should have pulled his clearance (if it ever should have been granted) once it became clear he was going to be separated from the army for cause, etc.
I hope his (transgendered, or gay, or something) sexual identity doesn't color public perception of the end of DADT; there are plenty of non-heterosexual members of the military who are not security risks. However, if he was getting separated over some "transition" related issues, that information would be relevant to a security clearance review in his particular case.