Any war inevitably involves casualties and some of these may be civilians. The nature of modern warfare, however, has led to a drastic increase in civilian casualties. Whereas in previous eras civilians would not be present at battles and the weaponry not powerful enough to cause much collateral damage, in recent times powerful weapons and less predictable battlegrounds mean civilian casualties are on the increase. So yes accidental civilian death is unavoidable within the current paradigm of the war on terrorism but rather than simply accepting this, there is very good reason to abandon the war on terrorism in its present formulation as soon as possible.
The war on terror is not really a war in the way the word has been understood for millennia - there are no clearly defined sides, no obvious material objectives and often the distinction between civilian and militant is on of degree of adherence to an ideal more than anything else. Combating terrorism in the middle east and south Asia relies almost entirely on the use of military intelligence to establish targets who are otherwise indistinguishable from the civilian population. In such situations it is impossible to avoid the occasional costly mistake. The US policy on this, as with everything else relating to the war on terror, tends towards acting first and evaluating later - always supported by the half-formed idea that the suspect might be about to launch an apocalyptic terrorist attack if not stopped immediately. This policy has led to numerous civilians being killed, tortured or imprisoned as suspected terrorist when they are not.
The second way in which civilians suffer through modern warfare is as collateral damage, usually in an urban environment. Despite the supposed extreme accuracy of modern weapons, many manage to end up destroying the houses of innocent civilians, often women and children. The reason for this is obvious; it is impossible, however accurate the technology, to drop bombs and missiles on a densely populated urban area without occasionally causing the deaths of innocent bystanders. This may be because the original target was inaccurate, because of an error in hitting the target or simply because civilians were in or very near to the target when it was hit. There are in fact countless examples of this from all outposts of the war on terror and the trend shows no sign of abating in the near future.
Aside from the clear moral problems of innocent deaths this problem is the cause of a much wider and more serious problem for the US war on terror. Every time a civilian is killed in their own country by US forces it will increase support for terrorist organizations. If the conflict is presented as one between a foreign, imperialist force with little reason to be there fighting against a militant rebellion (almost always conceived as in favour of the populous and its interests even if this is untrue) then gradually people will drift to the side of their fellow countrymen as the civilian death rate increases. The US tends to exacerbate the problem through a mixture of arrogance and complacency, not treating civilian deaths as the tragedy they are but as something inevitable ad therefore trivial compared to the grand ideal of spreading peace and democracy. The problem with this attitude is that it fails to acknowledge that any change in attitudes in troubled states must be accompanied by wholesale change among the people. The US is attempting to sell an ideal to a foreign people and in such a setting any collateral damage against this people will obviously make them disinclined to accept the sales-pitch.
While the manner in which the war on terrorism is conducted does make civilain casualties very difficult to avoid this is because the method is flawed and based on misconstrued motives from the beginning. While terrorism obviously must be stopped it is clear by now that he actions of the US and her allies since 9/11 have done more harm than good promoting a strong divide along religious and cultural lines and forcing many moderates towards extremism as a reaction against wholesale civilian death.