Governed MCP: Kernel-Level Tool Governance for AI Agents via Logit-Based Safety Primitives

AI agents increasingly call external tools (file system, network, APIs) through the Model Context Protocol (MCP). These tool calls are the agent's syscalls: privileged operations with side effects on shared state, yet today's safety enforcement lives entirely in userspace, where a 10-line script can bypass it. I propose Governed MCP, a kernel-resident tool governance gateway built on a logit-based safety primitive (ProbeLogits). The gateway interposes on every MCP tool call in a 6-layer pipeline: schema validation, trust tier, rate limit, adversarial pre-filter, a ProbeLogits semantic gate (the load-bearing check), and constitutional policy match, with a Blake3-hashed audit chain. I implement Governed MCP in Anima OS, a bare-metal x86-64 kernel in ~286,000 lines of Rust. The five non-inference layers plus the audit append cost a measured 11.3 us per call; the ProbeLogits gate (one probe-prompt prefill plus a single logit read) costs 332-556 ms per classification across Qwen2.5-7B, Llama-3-8B, and Mistral-7B, 2.4-3.4x faster than a Llama Guard 3 pass on the same hardware. A silicon-measured ablation shows that removing the ProbeLogits layer collapses F1 from 0.789 to 0.357 (delta-F1 = -0.432): hand-rule firewalling alone is insufficient. Every WASM-to-system host function and every registered MCP tool is mediated by the kernel gateway, so the 10-line userspace bypass that defeats existing guardrail libraries is structurally impossible; a disclosed set of ring-3 syscall paths remains ungated pending future work. Multi-model validation across three architectures (HarmBench 98-99% non-copyright block, XSTest 98.5-100% unsafe recall, ToxicChat parity with Llama Guard 3) shows the underlying primitive is architecture-agnostic. Governed MCP demonstrates that tool-call governance is feasible as an OS primitive, not just an application-layer concern.