Current industrial Internet of Things (IoT) demands are calling for more flexible and programmable networks that ensure high reliability in dynamic mission-critical scenarios. Centralized software-defined networking (SDN) offers high levels of flexibility and programmability that traditional distributed IoT protocols cannot offer. However, the use of SDN in IoT is currently not really lifting off due to wireless links unreliability, excessive control overhead, and devices limited resources. In order to reduce the impact of these issues, Whisper enables SDN-like capabilities in IoT by centrally controlling the distributed routing and scheduling planes in the IoT network (things overlay). To do so, the Whisper controller carefully sends computed messages compatible with the standardized distributed protocols already running in the network that change the default protocol-s behavior. However, as many other SDN-on-IoT approaches, Whisper is currently limited to the IoT network scope and remains as yet another independent network management silo. In this article, we argue that IoT network control should be jointly coordinated by the same SDN instance that also manages the wired segments. In order to do so, we present a new fully programmable solution that shifts the Whisper scope from the edge to the core, deploying and testing such architecture in real-world large-scale testbeds. We use 6TiSCH as industrial IoT enabler and the open network operating system platform to orchestrate all network segments. Finally, we report the technical challenges, discussing the lessons learned, and demonstrating the feasibility and suitability of this Whisper-based solution to provide an efficient and programmable end-to-end control over a heterogeneous network domain.