While advancements in Text-to-Video (T2V) generative AI offer a promising path toward democratizing content creation, current models are often optimized for visual fidelity rather than instructional efficacy. This study introduces PedaCo-Gen, a pedagogically-informed human-AI collaborative video generating system for authoring instructional videos based on Mayer's Cognitive Theory of Multimedia Learning (CTML). Moving away from traditional "one-shot" generation, PedaCo-Gen introduces an Intermediate Representation (IR) phase, enabling educators to interactively review and refine video blueprints-comprising scripts and visual descriptions-with an AI reviewer. Our study with 23 education experts demonstrates that PedaCo-Gen significantly enhances video quality across various topics and CTML principles compared to baselines. Participants perceived the AI-driven guidance not merely as a set of instructions but as a metacognitive scaffold that augmented their instructional design expertise, reporting high production efficiency (M=4.26) and guide validity (M=4.04). These findings highlight the importance of reclaiming pedagogical agency through principled co-creation, providing a foundation for future AI authoring tools that harmonize generative power with human professional expertise.