Doesn't this sacrifice the agent's ability to do non-deterministic natural language things? For example, if I want it to categorize all of my emails based on their content, is it going to fall back to writing a script that matches against a dictionary of keywords? That clearly wouldn't work as well. Maybe I am misunderstanding something here?

It’s no limitation at all, assuming it can read anything it prints. For example, if it wants to write directly to the user, it can run a program that only contains a print statement.