Coral reefs are on the brink of collapse, with climate change, ocean acidification, and pollution leading to a projected 70-90% loss of coral species within the next decade. Reef restoration is crucial, but its success hinges on introducing automation to upscale efforts. In this work, we present a highly configurable AI pipeline for the real-time deployment of coral reseeding devices. The pipeline consists of three core components: (i) the image labeling scheme, designed to address data availability and reduce the cost of expert labeling; (ii) the classifier which performs automated analysis of underwater imagery, at the image or patch-level, while also enabling quantitative coral coverage estimation; and (iii) the decision-making module that determines whether deployment should occur based on the classifier's analysis. By reducing reliance on manual experts, our proposed pipeline increases operational range and efficiency of reef restoration. We validate the proposed pipeline at five sites across the Great Barrier Reef, benchmarking its performance against annotations from expert marine scientists. The pipeline achieves 77.8% deployment accuracy, 89.1% accuracy for sub-image patch classification, and real-time model inference at 5.5 frames per second on a Jetson Orin. To address the limited availability of labeled data in this domain and encourage further research, we publicly release a comprehensive, annotated dataset of substrate imagery from the surveyed sites.