Edit: Okay i re-read the first post. Heck yea, floating around systems with your untagged character acting as a spy is fine. I assumed you meant joining opposing factions so as to gather intel on them. Sorry:)
I don't like characters as spies. You can spy easily enough just reading the message dumps on these forums or chatting people up.
Since there is absolutely no way to RP checking out someone's background (and if you tried they'd just RP that they checked out OK and not tell you they were spies), there isn't any defense against spies.
It's a non-defendable act for those being spied upon and a very bad idea IMO.
"To gain a hundred victories in a hundred battles is not the highest excellence;
to subjugate the enemy's army without doing battle is the highest of excellence."