I laid down rules ahead of time. Not being a big trek fan, other than a few episodes and movies I really liked, part of my deal for reff'ing a Trek game was: 1) tech consistency -- not rewiring crap into whatever you can think of. The application has to fit the piece of equipment you're using (so maybe using the transporter as a replicator, or the deflector dish as a tractor beam...); 2) canon's what I say it is -- I ignore the dumb stuf, most of TOS, STIV & V, much of the first few seasons of TNG, Voyager. For me, also, the utopian rhetoric is nice, but there's a reality behind it: Starfleet should have more of a military feel, there's real politics behind the UFP that aren't as shiny and humanitarian as portrayed...
So...set rules up front. Other than that, let them play.
"War is an ugly thing but not the ugliest of things; the decayed and degraded state of moral and patriotic feelings which thinks that nothing is worth war is much worse. A man who has nothing for which he is willing to fight, nothing which is more important than his own personal safety, is a miserable creature and has no chance of being free unless made and kept so by the exertions of better men than himself."
John Stuart Mill