In critical scenarios like natural disasters, the physical infrastructure of the network may be heavily damaged or completely torn down making difficult communications and rescue activities. In such cases, due to their nature, Unmanned Aerial Vehicles (UAVs) are usually employed to provide a temporary support network by forming a Flying Ad-Hoc Network (FANET). However, this network should be carefully monitored and safeguarded to guarantee its stability by deploying network security appliances, like Intrusion Detection Systems (IDSs). In the wake of these considerations, this paper delves into the utilization of IDS functions deployed on UAVs, named IDS-enabled UAVs, in emergencies leveraging the modern Software-Defined Network (SDN) paradigm. Specifically, the study proposes a dynamic approach to promptly activate IDS-enabled UAVs, in an SDN-FANET, responding to network traffic increasing and/or malicious activities taking place within the network. In order to achieve this objective, a Software-defined IDS with UAV Resource Aware Load Balancing strategy – SURA-LB – is proposed and implemented within the SDN controller, leveraging its programmable nature and its holistic view of the network. The SURA-LB strategy equally distributes the load among the set of IDS-enabled UAVs by considering their resources and energy utilization along with the experienced network traffic conditions. Finally, an extensive experimental campaign shows the benefits of the proposed load-balancing strategy in reducing and fairly distributing the workload among the IDS-enabled UAVs outperforming naive and baseline load-balancing strategies like Random and Round-Robin and, therefore, bolstering the resilience and the reliability of the set of IDS-enabled UAVs while the traffic to be monitored and analyzed increases.