It initially seems to be a strange combination of views that (a) killing in defense of the innocent is sometimes permissible, but (b) lying is never permissible, not even in defense of the innocent. Yet that is the predominant view in the Christian tradition. Does this mean that truth is more valuable than life? That doesn't sound right, at least not in general.
I want to try a very speculative solution to this paradox, one I don't want to fully endorse as it raises some further problems. Thomas Aquinas has an interesting position on the lethal defense of the innocent: only officers of the state are permitted to kill intentionally, while private citizens may use defensive means that they foresee could be lethal only if they don't intend death.
Why the difference? Well, here is my crazy thought: perhaps all instances of permissible intentionally lethal defense of the innocent are effectively instances of the death penalty. In emergency situations, where there is an imminent threat to innocents, the state authorizes its officers to execute aggressors on the spot, without the usual legal safeguards. Every instance of permissible killing in a just war is an execution--we just don't call it that, because the emergency context makes very different procedures appropriate. Note, further, that as we learn from John Paul II's Evangelium Vitae, the death penalty is only permissible when there are no other means to the defense of society. Thus the intentionally lethal means to the defense of the innocent can only be deployed as a last resort. That is why, say, prisoners of war are not killed--there is no longer a need for an emergency execution once they are disarmed.
Suppose that this eccentric theory of lethal police and military action is correct. Then it is easy to see why there is a distinction between intentional killing and lying. Permissible intentional killing is an act of justice, an imposition of a just penalty on an aggressor. If we add Boethian idea that it is an intrinsic benefit to one to have justice done to one, then the aggressor is directly benefited by being punished. But even without that idea, the distinction between a defensive act of justice and a merely defensive act seems significant. There is a fine Kantian thought that just punishment constitutes a showing of respect to the person being punished; but a lie is innately disrespectful to the rationality of the person lied to.
Still, the puzzle remains. Why is it that the greater harm of death is appropriate punishment while the lesser harm of being lied to is not? But not every harm is appropriate as a punishment, and sometimes a lesser harm is inappropriate as punishment while a greater is appropriate. Sometimes, this is for reasons of dignity. Thus, it is a lesser harm to lose one's arms than to lose one's life, but judicial amputation is barbaric and contrary to the dignity of the criminal (it is hard to fully explain this intuitive judgment). Sometimes, the lesser harm just wouldn't fit the crime, or maybe ven any crime. Suppose a politician misused her office. Public infamy could be fitting punishment. But while the harm to reputation is greater in public infamy than in gossip, it just wouldn't be a fitting punishment to have officers of the court gossip about the politician behind her back. In fact, being gossiped about simply doesn't seem to be the right sort of harm to be a punishment--maybe it is the essential isolation of it from the consciousness of the person being gossiped about that makes it be inappropriate. I have the intuition that being lied to is pretty much like that--it is essentially isolated from the consciousness of the person being lied to (it's not a lie if they tell you they're lying to you!), and it just doesn't seem the right kind of harm to be a punishment.
The difficulty with this account is that modeling intentionally lethal police and military action as a form of the death penalty suffers from serious problems. The main one is that we have good reason to think that many enemy soldiers, even if their side is opposed to justice, are likely to be non-culpable, because they are likely to be ignorant of the fact that their side is opposed to justice. Perhaps, though, in an emergency situation--and a war is always an emergency--the evidential standards can be much lower, and so we don't need to examine culpability. Another problem is that this account will not allow the police to engage in intentionally lethal action against a clearly insane attacker. But perhaps that's the right conclusion.