Rural defensive heritage sites are highly vulnerable assets that require decision-making under conditions of limited data and high uncertainty, particularly in the context of large-scale infrastructure projects and accelerating environmental processes. This study proposes a modular decision-support model for defining conservation priorities in a transparent, traceable, and data-sensitive manner, based on four selected fortress sites in the Yusufeli district of Artvin, Türkiye. The model employs a risk-based approach to quantify anthropogenic risks (AR) through the combined assessment of impact (I) and probability (P). Topographic and contextual vulnerability (TC) is structured through sub-indicators including visual dominance disruption, access discontinuities, landscape fragmentation, and microclimatic exposure, while material and intervention compatibility (MS) is evaluated as a distinct compatibility–risk component. These three modules are integrated through normalization and weighted aggregation into a single Priority Index (PI). In addition, the study introduces a Data Completeness Index (DCI) to explicitly address heterogeneity and gaps in field data, allowing prioritization outcomes to be interpreted with an associated confidence level. Laser-scanning-based documentation, deterioration mapping, and photographic records support the evidence-based construction of indicators. The proposed framework offers a transferable approach for generating intervention and monitoring priorities for rural defensive heritage under rapid landscape transformation, while explicitly managing data uncertainty rather than obscuring it.