Programmable Logic Controllers (PLCs) execute critical control software that drives Industrial Automation and Control Systems (IACS). PLCs can become easy targets for cyber-adversaries as they are resource-constrained and are usually built using legacy, less-capable security measures. Security attacks can significantly affect system availability, which is an essential requirement for IACS. We propose a method to make PLC applications more security-aware. Based on the well-known IEC 61499 function blocks standard for developing IACS software, our method allows designers to annotate critical parts of an application during design time. On deployment, these parts of the application are automatically secured using appropriate security mechanisms to detect and prevent attacks. We present a summary of availability attacks on distributed IACS applications that can be mitigated by our proposed method. Security mechanisms are achieved using IEC 61499 Service-Interface Function Blocks (SIFBs) embedding Intrusion Detection and Prevention System (IDPS), added to the application at compile time. This method is more amenable to providing active security protection from attacks on previously unknown (zero-day) vulnerabilities. We test our solution on an IEC 61499 application executing on Wago PFC200 PLCs. Experiments show that we can successfully log and prevent attacks at the application level as well as help the application to gracefully degrade into safe mode, subsequently improving availability.