Software-defined networking (SDN) centralizes and abstracts network control, potentially introducing single points of failure. To enhance scalability and flexibility, a distributed SDN (DSDN) approach is essential. This research introduces MLB-DSDN, an energy-efficient multipath load-balancing protocol for flow control in DSDNs, with a specific focus on an eco-friendly aerial computing environment. MLB-DSDN protocol identifies multiple routes between source and destination nodes, dynamically distributing data packets based on an inverse proportionality mechanism relative to route traversal time. This strategy balances traffic loads across various channels, significantly reducing the total routing time for data packet delivery. Moreover, the proposed framework enhances network performance and resilience in dynamic, high-mobility environments. It achieves this by incorporating autonomous aerial vehicles (AAVs) and satellite nodes as mobile network components. Experimental results demonstrate that MLB-DSDN improves average response time by 14.40% and increases average transactions per second by 14.63%, surpassing state-of-the-art methodologies. The integration of AAVs and satellites contributes to an additional 10% improvement in network throughput and a 12% reduction in latency compared to ground-based solutions alone. These findings highlight the robustness and efficiency of MLB-DSDN in enabling seamless and reliable data dissemination across terrestrial and aerial networks. Thus, the proposed framework enhances scalability, reliability, and flexibility in aerial computing, offering a robust and adaptable solution for resilient modern networks.