(I'm having some trouble getting the hang of quote tags on these forums, hopefully the following is a halfway legible back and forth, I'm trying to make the quoted bits show up better by bolding and italicizing them.)
"Fine and good, Critias; but here's the situation: two good nations in d'nd go to war with each other (foul manipulations of chaos and evil have done their wicked work); both good nations sport armies of paladins; these armies face-off on the field of battle to protect their respective nations' peoples; now what?"
Depends on the precise setting. Sometimes? They all start losing holy powers, because they're putting nationalism ahead of their (presumably shared?) faith. If nothing else, some of those Paladins are going to bust out "Detect Evil" (which they can do at will) and start to scratch their heads when NO ONE on the opposite side is pinging their radar. If not, they're gonna start to Smite Evil to try and get some extra damage in, and it's not gonna work, and eventually folks will realize they're being toyed with, y'know? Because "Good" and "Evil" are very real concepts in D&D's fairly simplistic morality system, and that means sooner or later someone as hardcore as a Paladin is gonna either realize what's going on, or their deity of choice will. Goodly gods tend to be smarter than evil ones in most D&D fiction (or "wiser," at least), so the odds are good the horrible crisis is somehow averted. But the fact is that if armies of paladins are clashing, someone's gonna be in some holy trouble for it (and the odds are also good that it took some large scale manipulation from the forces of evil and blah blah blah the book's protagonists probably solve anything).
The point, though, is that neither side BECOMES Chaotic Evil just because they've having a spat. It's a tragedy and all that, but the fact remains that the alignment stat on all those characters still probably stays Lawful Good, and the societies they represent are still full of NPCs that are still LG, NG, or LN (or whatever, basically likely just one step away from the "default" LG of their presumed empires).
"Now, don't get me wrong: I feel your idealism, i do; and, by all means, maintain this idealism in d'nd (or, indeed, in whatever game you please); I'm not even saying it's not appropriate (in fact, morality does by necessity require teaching; it's too easy to countermand our instinctive morals with convenience or expedience); I'm just saying that the d'nd alignment system is logically inconsistent - an absolute system is flawed, inherently."
Well, no. I'm not idealistic about it, I'm just staying how it works in D&D. I think it's silly, even in D&D, but if it works anywhere it's in that cliched "good versus evil" type of high fantasy setting. Moral relativism changes opinions in D&D, but not alignments. Because alignments are real, afterlifes are real, extraplanar beings are real, and it's all got very tangible in-game effects (and all based on one strange little statistic, your alignment). You said it WASN'T an absolute system earlier, which was what I was taking umbrage to. Real life morality is based on convenience, expedience, and the manipulation of those who tell us what to think; D&D morality, by nature, isn't, due to the inherent supernatural nature of the setting and the way SO MANY powers are based on alignment.
"The flaw in mindlessly following the Codex, though, is that yer enemy knows exactly what yer gonna do...."
That's not necessarily the case with a text the size of the Codex, though. The descriptions for it normally say something like "for every conceivable tactical situation a Marine may find himself in, there are hundreds of pages of text!" That means you've got options, and THAT means you're not mindlessly following anything. If the ideal tactical solution that Guilliman wrote down is a flowchart with a hundred variables and a hundred different options based on each one, no one's going to know JUST what you're going to do. Someone would need to know ALL those options, and know which one is your particular Ultramarine's favorite, and know just what resources the Ultramarine has, in order to know what he'd do.
I mean, the codex advice could be largely theoretical in some situations, it could be quite specific in others, we don't know (because none of us have any idea of what's really in the book). But if the advice is some Sun Tzu stuff like "attack where the enemy is weak," well, that doesn't give the enemy much to go by. He doesn't know where you perceive him to be weak, he doesn't know what you have to attack with, he doesn't know when you'll attack, etc, etc.
It's hard for us to call the codex a straightjacket because for all we know -- and, again, based on the one quote of it I recall seeing, it really IS, at least in part, theoretical Sun Tzu stuff -- it could be a really comfortable, roomy, coat instead, with plenty of pockets to choose from and lots of breathing room. 
