To answer the questions: Yes, they were all Trek familiar, playing Starfleet officers. Although my players have seriously considered going freelance more than once, they eventually rejected it on the grounds that Starfleet would probably make them give up most of their "cool toys" if they resigned. But this all went down back in the mid '90's when the Taliban was just rising to power, and "honor killings" were in the news.
And we're skating the edge of politics here, so I'll kill that topic now.
ANYWAY...
Besides General Orders and Regulations, many ships are likely to have their own, ship-specific "standing orders" (probably not the right word for them) that depend upon the Captain's personal style of running his ship. I think one of the old LUG books mentioned these types of orders (such as how to address the Captain, etc.)
Barring overriding Orders or Regulations, the level of permissible fraternization probably falls under that purview.
I am suddenly reminded of a favorite Denis Leary routine:
Another thing when I’m President, by the way... You wanna join the military, any branch, army, airforce, marines, navy. Once you join you can **** whoever you want. Other soldiers, superior officers, I don’t give a flying ****, **** your brains out. Go ahead, you have my permission. As long as you want to kill the enemy, you can have sex with whoever you like. “I like to **** other guys”, “Here’s another guy and a gun. Go go go!”. “I like to **** sheep”, “Here’s a sheep and a gun. Go go go!”. “I like to **** watermelons”, “here’s a watermelon and a gun, Go go go!”. **** ‘em, kill ‘em, an' eat ‘em boys, go ahead.
"It's hard being an evil genius when everybody else is so stupid" -- Quantum Crook