I think there is a difference morally between soldiers and civilians. Of course there can be terrorist attacks on soldiers also, and often are, but soldiers are to a degree prepared to deal with violence and are appropriately equipped in material terms also. Civilians are in principle only indirectly involved in the conflict and so should not be harmed. This is even the case where the civilians are full of hatred for the cause espoused by the terrorists while soldiers are not. It is even true when attacking civilians is very effective in ending the conflict sooner. Unless we restrict who shall be harmed in a conflict then potentially anyone could be harmed and this is immoral.
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Is terrorism worse than conventional warfare? My initial response is "yes," but on reflection I'm not sure. A soldier's life is surely worth no less than a civilian's, so why should it be preferable that the former die instead of the latter?