First please understand I very much against abortion, war and any violence. Having said that I’m not convinced the distinction is one that matters between these two scenarios.
The ultimate goal of aborting a fetus that threatens the life of a mother is the same as the goal of shooting down a plane on 9/11. In both the goal is to save innocent lives. In both possibly innocent lives will be killed.
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There is a difference between the end of an act and the goal, and between those two and the result.
An action is taken to fulfill a goal, to save one or more lives. the result is, one hopes, the saving of the life, but it may not be, as you point out.
The end of the action is what you might call the goal of the action in itself.
You are driving when you see a car hurtling down a hill towards a group of people. You quickly intercept the car with yours, knocking off course into a river. If the car is empty, no one dies. If the car is full of people, they die (in this scenario). You did not, however, intend their deaths, nor was death the end of your action. The end of your action was knocking the car. The goal was to save the lives of the bystanders. The result was some saved lives and some lost if there were people in the car, or just saved lives if it was empty.
In shooting down the planes, if they are empty, you will still want to shoot it down. The end of you actiin is the disablement of the plane, the goal is to save lives the plane might take.
But in abortion, while the goal is the same, to save the life of the mother, the end of the act is different. The act just
is the taking of a human life, the end of the act is the death od the baby.
Consider is a doctor performs chemo on a woman with cancer. the end is to eradicate the cancerous cells, but a side effect for a pregnant woman might be that the unborn child dies.
Does that clarify the difference for you?