Let's say you have a jq MCP. How do you pass data in and out to/from it without the data also being processed as tokens?

That's really my only issue with MCPs.

With shell you can pass data from one component to another directly, not only being cheaper, faster, but also preserving complete integrity. While models nowadays seem to do data echoing well, there's always the chance they might not do it exactly.

There's no reason why a shell would not be able to limit abilities of a party using it as well, by virtue of just implementing only the desired functionality. What makes it more advanced in this context is the (standard) ability to express how to connect multiple components to each other, or to/from local storage. MCP does not have this.

Providing that does not have any inherent danger any more than jq's functions have an inherent danger. Actual execution of processes or real files does not need to be involved.