1. A computer-implemented secure application execution system having computer readable media that store executable instructions executed by a processor, comprising: an isolation container in which an isolated application runs in isolation from a non-isolated application, the isolated application and non-isolated application both running in association with a single operating system (OS); and an isolated OS subsystem of the isolation container that provides services to the isolated application, and a non-isolated OS subsystem of the OS that provides services to the non-isolated application, the isolated OS subsystem and non-isolated OS subsystem providing equivalent services to the corresponding isolated application and non-isolated application.