The new culture of networked systems that offer everywhere accessible services has given rise to various types of security trade-offs. In fact, with the evolution of physical systems that keep getting integrated with cyber frameworks, cyber threats have far more critical effects as they get reflected on the physical environment. As a result, the issue of security of cyber physical systems requires a special holistic treatment. In this paper, we study the trade-off between security, safety and availability in such systems and demonstrate these concepts on implantable medical devices as a case study. We discuss the challenges and constraints associated with securing such systems and focus on the trade-off between security measures required for blocking unauthorized access to the device, and the safety of the patient in emergency situations where such measures must be dropped to allow access. We analyze the up to date proposed solutions and discuss their strengths and limitations.