Current Software Defined Networking (SDN) techniques allow improving network control and flexibility. However its use in IoT is not trivial because IoT networks are unreliable and highly resource-constrained. Among some of the existing solutions proposed in the literature, Whisper enables SDN-like control over the packet forwarding and cell allocation of IoT devices by injecting in the network artificial, but still standard compliant messages that alter the default protocol behavior. Since Whisper uses carefully computed routing and scheduling messages that are compatible with the distributed protocols run in the network, it reduces the overhead in the network and operates without modifying the IoT devices' firmware. However, as other SDN-on-IoT technologies, Whisper is currently limited to the IoT network scope and remains as yet another independent network management silo. In this paper we propose a new higher-level architecture that allows to fully integrate the IoT SDN network management into a network operating system, such as ONOS, by using Whisper in order to provide an integral end-to-end softwarization. We also describe the interaction between the Whisper platform and the orchestrator and test our solution with real 6TiSCH-compatible hardware in the ONOS platform. Finally, we discuss the requirements and technical challenges to fully leverage Whisper to provide an efficient and programmable end-to-end control over an heterogeneous network domain.