Scientific diagrams convey explicit structural information, yet modern text-to-image models often produce visually plausible but structurally incorrect results. Existing benchmarks either rely on image-centric or subjective metrics insensitive to structure, or evaluate intermediate symbolic representations rather than final rendered images, leaving pixel-based diagram generation underexplored. We introduce SciFlow-Bench, a structure-first benchmark for evaluating scientific diagram generation directly from pixel-level outputs. Built from real scientific PDFs, SciFlow-Bench pairs each source framework figure with a canonical ground-truth graph and evaluates models as black-box image generators under a closed-loop, round-trip protocol that inverse-parses generated diagram images back into structured graphs for comparison. This design enforces evaluation by structural recoverability rather than visual similarity alone, and is enabled by a hierarchical multi-agent system that coordinates planning, perception, and structural reasoning. Experiments show that preserving structural correctness remains a fundamental challenge, particularly for diagrams with complex topology, underscoring the need for structure-aware evaluation.