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The adoption of software defined networking (SDN) within traditional networks has provided operators the ability to manage diverse resources and easily reconfigure networks as requirements change. Recent research has extended this concept to IEEE 802.15.4 low-power wireless networks, which form a key component of the Internet of Things (IoT). However, the multiple traffic patterns necessary for SDN control makes it difficult to apply this approach to these highly challenging environments. This paper presents Atomic-SDN, a highly reliable and low-latency solution for SDN in low-power wireless. Atomic-SDN introduces a novel synchronous flooding (SF) architecture capable of dynamically configuring SF protocols to satisfy complex SDN control requirements, and draws from the authors' previous experiences in the IEEE EWSN Dependability Competition: where SF solutions have consistently outperformed other entries. Using this approach, Atomic-SDN presents considerable performance gains over other SDN implementations for low-power IoT networks. We evaluate the Atomic-SDN through simulation and experimentation, and show how utilizing SF techniques provides latency and reliability guarantees to SDN control operations as the local mesh scales. We compare the Atomic-SDN against the other SDN implementations based on the IEEE 802.15.4 network stack, and establish that the Atomic-SDN improves SDN control by orders-of-magnitude across latency, reliability and energy-efficiency metrics.