I know of one person, at my former company, who was
denied by NSA, and ended up getting cleared through
the NRO, in Reston, Va.   If you didn't admit to anything
horrible, then your DoD clearance will probably be ok -
just be honest with the DoD folks, or they will deny you
on "personal conduct".   I used to feel bad, about my
situation at the NSA, but now I no longer care, and I am
much happier dealing with other agencies.  The NSA is
a really dysfunctional place to work - people with
unresolved anger/issues, inappropriateness, etc.  To
give you an example, one of my old assistant
work-center chiefs had a beef with his boss; their desks
were next to each other, so very early one morning, he
came in, before his boss, and kept slamming his chair
against his boss's desk screaming, "get the f--- out of
my face".  I came very close to calling the NSA police.

Funny thing, after all my years there, I never figured out
what all the fuss was about - too many people, reading
too many Tom Clancey books !