Realization of logic and storage operations in memristive circuits have opened up a promising research direction of in-memory computing. Elementary digital circuits, e.g., Boolean arithmetic circuits, can be economically realized within memristive circuits with a limited performance overhead as compared to the standard computation paradigms. This paper takes a major step along this direction by proposing a fully-programmable in-memory computing system. In particular, we address, for the first time, the question of controlling the in-memory computation, by proposing a lightweight unit managing the operations performed on a memristive array. Assembly-level programming abstraction is achieved by a natively-implemented majority and complement operator. This platform enables diverse sets of applications to be ported with little effort. As a case study, we present a standardized symmetric-key cipher for lightweight security applications. The detailed system design flow and simulation results with accurate device models are reported validating the approach.