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Happy to discuss further. I'll try and get a new patch done today that disables the handler for any threads Python creates a thread state for. The change to _Py_VERIFY_FD will still be there, but the begin/end suppress will go (using the verify function to protect CRT calls can go completely once we are prepared to force people to build with VC14, but I want to avoid that for as long as possible while we transition).
Also notice that Verify_fd is a race condition but was the best solution available at the time. I'm keen to see it go.
As far as a better solution goes, I've discussed this in depth with the main CRT developer at Microsoft and there won't be one. The best concession I could get was the thread local handler so we can disable it locally rather than process wide.