Embodiments provide a system and method for reasoning about the optimality of a configuration parameter of a distributed system. During operation, the system obtains a multi-layer graph for a system with a plurality of components, wherein the multi-layer graph comprises a configuration subgraph, a vulnerability subgraph, and a dependency subgraph. The system determines, based on the multi-layer graph, constraint relationships associated with configuration parameters for the components, wherein the constraint relationships include security constraints and functionality constraints. The system computes an unsatisfiable core which comprises a set of mutually incompatible constraints. The system resolves, based on a strategy and over multiple iterations, the unsatisfiable core by analyzing one pair of mutually incompatible constraints per a respective iteration, to obtain a new unsatisfiable core which comprises a smaller number of mutually incompatible constraints than the computed unsatisfiable core or a previously computed unsatisfiable core from a most recent iteration.