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Due to frequently changing requirements, the internal structure of cloud services is highly dynamic. To ensure flexibility, adaptability, and maintainability for dynamically evolving services, modular software development has become the dominating paradigm. By following this approach, services can be rapidly constructed by composing existing, newly developed and publicly available third-party modules. However, newly added modules might be unstable, resource-intensive, or untrustworthy. Thus, satisfying non-functional requirements such as reliability, efficiency, and security while ensuring rapid release cycles is a challenging task. In this paper, we discuss how to tackle these issues by employing container virtualization to isolate modules from each other according to a specification of isolation constraints. We satisfy non-functional requirements for cloud services by automatically transforming the modules comprised into a container-based system. To deal with the increased overhead that is caused by isolating modules from each other, we calculate the minimum set of containers required to satisfy the isolation constraints specified. Moreover, we present and report on a prototypical transformation pipeline that automatically transforms cloud services developed based on the Java Platform Module System into container-based systems.