replied to your quote “As Jim [Spahr, Office of Naval Intelligence] learned his job better,…”
In those days, if an individual passed initial scrutiny and received a security clearance, particularly if it involved special intelligence and they were later discovered, they lost their clearance and were discharged from the military. While they may not have had a wife or husband, they had parents or siblings and credible threats, in addition to their being outed could be made to coerce them into giving information away. They were in fact considered serious risks.
Except the military accepted some gays and not others. When not at war, there were purges of gay service members, and during war gay service members were very often looked over. The military decided when it was convenient to target gay service members. The military decided when to consider them serious risks.
Not to mention that the quote is talking about the FBI tracking civilians because of their sexuality.
Let me pose a question: Why should gay service members be any more likely than straight service members to betray their country?
There are a great many things that straight service members would certainly like kept secret (extramarital affairs come to mind), but they are not singled out like this.
Aside from wanting to keep their sexuality private, this branding of gays as security risks stemmed in large part from wildly inaccurate assessments of gay characteristics. This includes the idea that gay men were self absorbed and would talk about themselves given any opportunity. There were no facts involved.