The Model Context Protocol (MCP) has become a leading standard for connecting Large Language Models (LLMs) to external tools, software, and data sources. MCP architecture favors ease of integration over security, blending the data and control planes into a single natural language channel. This introduces confused deputy and prompt injection vulnerabilities that cannot be completely mitigated in the software development lifecycle (SDLC) of an MCP server. Structured security guidance for server developers has been outpaced by this adoption trend, leaving them without a clear way to identify where vulnerabilities can be addressed at the server layer and where architectural constraints create hard limits. This paper presents a framework based on OWASP MCP Top 10 mapped to three architectural tiers, developed using Design Science Research (DSR). Vulnerabilities are classified as server-primary, gateway-primary, or protocol-primary applying a cascading decision tree following four questions, resulting in reproducible tier assignments and confidence levels independent of who applies it. The framework was validated against an enterprise-grade Managed File Transfer (MFT) MCP server built in Go. Validation results showed that high-confidence server-tier controls worked as predicted, and low-confidence protocol-tier controls failed for architectural reasons beyond server implementation. The architectural ceiling encountered during practical validation is the main contribution and shows how secure-by-design development can reduce the MCP attack surface but not completely mitigate it.

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