Organizations have responded to the pandemic caused by the SARS-CoV-2 with a very wide range of management functions and capabilities: risk management, crisis management, emergency management, business continuity management and disaster management. Common to all of them is decision-making in situations of high uncertainty based on the assessed risk. Given available data from the World Health Organization that six months after pandemic had been declared, the number of patients and deaths is constantly increasing, the question arises whether the lack of key information on risk in conditions of high uncertainty caused by coronavirus, in paralel with the complexity of modern (natural, social, technical) systems and their interactions, has issued the application of the traditional concept of risk management based on historical data, statistics, and cost-benefit analysis. Based on the assumption that in conditions of uncertainty and non-routine environment, risk-based decision making process in complex systems suffers from numerous shortcomings, we will review the practical and methodological limitations of this concept through key stages of the risk assessment process. At the same time, the aim of this paper is to point out the advantages of applying the concept of organizational resilience in managing complex systems, starting from the fact that immune systems and resilient organizations are the most effective response strategy to non-routine risks (low frequency events and catastrophic consequences). The basic changes we propose in the process of managing the non-routine risks of infectious diseases that led to the crisis caused by the SARS-CoV-2 pandemic are based on the conclusion that the anticipatory strategy aimed at predicting events needs to be "expanded" with a system resilience strategy. This does not diminish the importance of a risk-based decision-making approach in conditions of uncertainty.