Systems composed of a fleet of autonomous mobile robots are among the most complex control systems. This control complexity is at a high level especially when those robots navigate in hazardous and dynamic environments such as chemical analysis laboratories. These systems include different dangerous and harmful products (toxic, flammable, explosive...) with different quantity. In order to perform its mission on a regular basis, this multi-robot system can be controlled according to multiple architectures. We propose, firstly, to apply the System Theoretic Process Analysis (STPA) on two selected control architectures, namely distributed and hybrid architectures in order to obtain a set of loss scenarios for each kind of architecture. For further assessment, the Analytic Hierarchy Process (AHP) is used to choose the best architecture. The proposed approach provides a risk analysis and a more practical comparison between the two control architectures of a mobile multi-robot system and facilitates decision-making, even in complex situations.