Anyone who's ever `DROP TABLE`d on a production rather than test database has encountered the same problem in meatspace.
In this context, the MCP interface acts as a privilege-limiting proxy between the actor (LLM/agent) and the tool, and it's little different from the standard best practice of always using accounts (and API keys) with the minimum set of necessary privileges.
It might be easier in practice to set up an MCP server to do this privilege-limiting than to refactor an API or CLI-tool, but that's more an indictment of the latter than an endorsement of the former.