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It sounds to me like `PyInterpreterState.eval_frame` is being used to lazily modify the bytecode to support breakpoints.
I can see no reason why changing the bytecode can't be done via `function.__code__`.
Suppose the code-object with the breakpoint add is `bcode`, then to turn on the breakpoint:
original_code = f.__code__
f.__code__ = bcode
and to turn it off
f.__code__ = original_code
The JVM supports bytecode instrumentation (via class loaders). It works well, as it provides a clear way for third party tools to modify the behaviour of a particular piece of code without violating any of the invariants of the interpreter. 
We don't really advertise setting `function.__code__` as a way to add low-impact breakpoints or profiling, but it is there.
If this use case is important, and it sounds like it is, then a better option would be to offer library support for adding and removing breakpoints/instrumentation.
This would have the advantage of being composable in a way that changing `PyInterpreterState.eval_frame` is not; in other words, it would be possible for one tool to add profiling and another to add breakpoints and have both work correctly.
I can write up a PEP if necessary.