I like this kind of stuff.
A particularly interesting take on this is tailspin, although the repo appears have been taken down: https://github.com/wthimbleby/tailspin That one offered a reversible JavaScript debugger written in JavaScript, which I thought that was very impressive from a technical standpoint.
MetaJS has some open issues - some related to the fact that it's intended to let you step through code, which I think makes certain interop scenarios difficult (let's say for example native code calls MetaJS code and expects a return value - it's not possible to set a MetaJS breakpoint there because the native runtime isn't paused).
I would be curious to know how MetaES fares under something like test262. I think a metacircular interpreter that does well in an extensive suite like that could indeed be a proper, "safe alternative to eval" (as suggested by another commenter).
https://github.com/metaes/metaes - "MetaES was tested using test262 test suite. Runnable test suite is currently not added to the repository."
You're right about breakpoints while code is called by native functions. That's something that should be discussed more.