Mmm.. you did not say yet why you are against this feature, other than "the lib *should not* use non-daemonized threads"

This sounds like "the lib should not use feature X in Python because it will block everything"

And now we're proposing to remove the limitation and you are telling me I am vague and unreasonable.

Let me try differently then.

Consider this script to be a library I don't control. I need to call the .stop() function when my main application shuts down. 

I can't use signals because you forbid it in mod_wsgi

How do I do, since asking the person to daemonize his thread is not an option ?

I see several options:
1 - monkey patch the lib
2 - remove regular threads from Python, or making them always daemonized
3 - add an atexit() option in threads in Python
4 - use signals and drop the usage of mod_wsgi

I think 3- is the cleanest.