Anyway, we can evaluate the permissibly of moral actions using the principle of double effect. As you suggest, we do not always have the luxury of choosing courses of action without some kind of negative side effect. At the same time, it is not morally permissible to engage in intrinsically immoral acts (sorry, utilitarians/consequentialists) nor is it permissible to intend the evil effect. We may also not use the evil effect as a means of attaining the desired good. Finally, there must be a proportionality between the good and bad effects that justifies the toleration of the bad effect.