One of the trickier concepts within traditional Catholic moral theology is that of "double effect". The basic idea here is, one may perform certain actions with a morally acceptable intent, despite that the fact that certain undesirable results are known to be almost certain to result as well.
Thus, according to classic moral teaching, it is unacceptable to will to kill another person, but it acceptable to will to stop an intruder from threatening your family by pointing a .45 automatic at him and pulling the trigger. (I'll use the example of self defense throughout, since that's one of the most classic examples of double effect.) Your will is to stop him from causing harm, while his death (if it occurs) is a foreseen but undesired consequence. (Thus, one goes from self defense to murder if the intruder is writhing helplessly on the ground after the first shot and you step over and fire a second shot to finish him off: There is no sense in which such an action is necessary for self defense, and so the only possible object of your action is to kill the now wounded assailant.)
Now, the principle of double effect clearly handles some very important moral questions, and I don't for a moment want to sound like I'm saying it doesn't make sense or should be thrown out. However, it does seem to present a certain potential for tying ones self up in mental knots.
I think the trouble area tends to be the "undesired but foreseen" element of the double effect. A lot of people seem to have difficulty with the idea of foreseeing something clearly as the result of an action without actually willing it. Thus, in cases of self defense, some err on the side of saying that one cannot justify any defensive action which one can foresee with near complete certainty will result in the death of the attacker. Others err in the other direction, believing that by virtue of being an attacker, the assailant in a self defense situation essentially cedes his life, and any action against him is justified.
The right balance, I think, is to understand that the killing of an attacker is morally justifiable only to the extent that it is necessary in order to achieve the goal of defending the innocent. One the one hand, the principle of double effect does not require that a defender hold back on the force he uses, so long as the use of greater force actually achieves defense with more certainty. And yet, once the threat is averted, further use of force is not morally acceptible.