An apparatus in one embodiment comprises a host device that includes at least one processor and an associated memory. The host device is configured to implement a plurality of containers each configured to access one or more portions of the memory. The containers are implemented as respective kernel control groups utilizing operating system level virtualization of the processor of the host device. The host device is further configured to assign the containers to groups in accordance with one or more designated criteria, and to generate checkpoints for respective groups of the containers. In conjunction with generation of a given one of the checkpoints for a particular one of the groups of containers, the host device identifies one or more pages of the memory that are shared by at least first and second containers of the particular group of containers, and generates the given checkpoint without duplicating the one or more shared pages to persistent storage.