After Bradley/Chelsea Manning do you think they would do anything else?
What gets/got people failed for security clearances wasn't that they were gay (or had a drinking/gambling/whatever problem), was that it made them vulnerable to blackmail and exploitation by espionage agents. Basically, secrets you didn't want anyone else to know about.
Wilson wasn't honest, he deceived and lied by omission by not revealing he was genetic female, which is required/expected under current regulations. That is what rightfully got him fired. He really should have known that he wouldn't be able to get away with passing indefinitely.
The whole question of if trans folks should be allowed to serve is a different question. I mean, he is a good example that trans people CAN serve just fine, but the counterpoint is that GID also compromises their judgement. If that is simply because of the unfair treatment, or something deeper? That is a complication to that question.