Its not really something I've put a great deal of thought into, but it just seems fairer and more honourable (note, not necessarily reaching the status of 'honourable', just moreso) to attack someone who has the capacity to defend themselves rather than 'innocent' civilians.
If there really is an intent to attack or punish the populace, then they should at least be warned that war has been declared.
Then again, the terrorists would probably counter that by saying that the people imprisoned/killed/etc weren't given any warnings, so in actual fact they're being perfectly fair, so I dunno!