[EDIT: This is what I had written, while Tarion was busy digging up the actual cite]
Starion,
Here's a question for you: what if we just read the two books side by side?
"Codex over Rulebook" may be the inviolate way that many people play the game, but it's not persuasive absent some kind of errata-level statement by Games Workshop or an explicit statement to that effect in a rulebook. I haven't been playing the game long enough to know if there was ever such an authoritative statement, but I wouldn't be surprised if this was one of those things that the community has just accepted as inviolable since time immemorial because ... well, because the community has just accepted it as inviolable since time immemorial, and it's a reasonable approximation of what the rules actually say.
So let me ask you this: what if neither is, by default, authoritative?
Neither of the two cases you cite are literal conflicts. In the case of space marine special characters, SeattleDV8's/Jwolf's answer (i.e., p. 49 of the rulebook) doesn't depend on CoR vs. RoC. Codex: Space Marines doesn't explicitly say that you can take two named characters, after all. It only fails to place the "Unique" special rule in the right place. Page 49 doesn't depend on a named special rule at all.
Similarly, the *H codices' versions of force weapons aren't literal conflicts with page 50. The *H codices describe what force weapons chosen from those codices do, which includes "slaying outright," and page 50 says that force weapons grant an extra psychic power, which functions as described, which includes inflicting Instant Death. Read the two as equally authoritative and you end up with *H force weapons that can, if you pass a psychic test, slay en enemy outright, and can, if you pass a psychic test, inflict Instant Death. I see no reason why the *H force weapons can't essentially grant their bearers both powers.
This "side by side" interpretation would mean that the March 2009 FAQ on dedicated transports is wrong, as that answer directly conflicts with page 67 ("The only limitation"). But that's a FAQ, not an erratum.
As always, I think that player agreement is the best way to go. As a textual matter though, and if for some reason we feel the need to articulate an inviolable principle, in the absence of an authoritative statement or a really convincing proof that either CoR or RoC is necessary to make the game work, it seems to me that the most natural approach is to treat SbS as the default state of affairs.
EDIT: Ah, I see Tarion finally found the citation. Good enough for me.