A single Uriel could still level in the entire world in 27th Century. A 5000-megaton Harbinger's environmental effects remain unchanged; one significant FS bomb is enough to wipe out a city, a large one could take out an entire seaboard of the US, and we've got no evidence a city has gotten massively tougher by FS-time. In our own lifetime we've actually seen the reverse take place as we've moved away from stone as a building material.
Pissing off your pilots carries a great deal of danger in the FreeSpace setting. There are too many of them and they are called on to use their weapons in situations too fluid to tightly control it the way we do modern nuclear weapons, yet they wield more destructive power than the nuclear arsenals of modern nations. Even if they only launch a single missile, that's still going to be several kilotons of raw destructive power at the least. That'll take down a few blocks minimum, I don't care what your building materials are, they're civilian buildings.
That's fair enough, but these craft are mostly employed in situations where such an event is unlikely to take place. And fair enough, they have the potential to level something important, but who's to say these guys are actually going to do such a thing? They don't recruit the closest person they see for aircrew, the selection process is quite rigorous in nature, and if someone can't take the stress of combat, they're most likely going to fail the recruitment process. Combat is stressful, so we recruit people who can handle it, and employ strategies to deal with Combat Stress (Units being rotated from the front-lines every 30 days etc.) And besides, psychological support is a must on the frontlines, and I'd imagine it'd be there in spades by the 27th Century. Someone getting pissed off enough to level a planet should not happen when we're talking about people who've been picked because they can survive this kind of stuff (among many other things).
Sparta and the Theban Sacred Band would both like to discuss your assumptions with you. We're clever monkeys, we humans, and we've worked out how to make such relationships work for us in building the unit up, or at least kept them from causing problems, before. Similarly, your comment about loose discipline creating a lack of espirt-de-corps does not follow; it's possible for a unit to have plenty of elan but no discipline.
Well with the TSB, do we know if lovers favoured one another over the rest of their unit? It may have been their individual ability as soldiers which made them effective, rather than their unit cohesion, the latter being essential in modern warfare. Esprit-de-corps is a small part, but it is one of the aims of discipline in the military, I mean, the stereotypical Marine doesn't shout OORAH because his platoon is a bunch of partyboys, discipline helps foster the pride of a professional unit and maintain that professional status.
Also, I think you willfully ignored my point that we can't stop this kind of behavior now even in well-disciplined militaries, yet as whole it does not do great damage to the the warfighting efficency of the units involved; we pounce on it because it could but in the end we're fighting a losing battle as long as our soldiers aren't robots. As long as real discipline, taking orders and carrying them out, is maintained, what does it matter who screws who? If the UEF can train its people to handle that sort of environment, which is most likely quite possible, then more power to them; they're probably better off for it than the modern setup.
Oh sorry, I didn't "willfully ignore" it as such, but when you take the hard-line in the military, at least it acts as a deterrent for that kind of behaviour. It's better that you discourage that kind of behaviour rather than condone it, in my opinion. Well it's not the physical act that's the issue here (although it can be an issue on the frontlines where no contraception is available), but the feelings that go with it. Those feelings of attachment or lust, love, and whatnot, have the power to interrupt the real discipline. It's situations like where the pilot has to act on his own initiative, (sorry for self quote)
"Should I assist the pilot I have sexual relationship with, or the other pilot I don't have a sexual relationship with."
You have the notion to protect the one you're intimate with, rather than the most logical action. So the UEF can train its people to **** one another, but lose all feelings of attachment in battle? Fair enough, that may be possible, but in combat learned behaviour gives way to instinct, and you have the potential of all that biting you in the ass.