I've removed the invocation of the wrapper code in our project, but the issue has not exhibited itself. This leads me to suspect a few possibilities of things that have changed since we had the issue in June:

1) Distribute was updated with its fix for this issue. I don't expect that code was being called in our application, but I didn't strictly rule it out.
2) The application launcher was changed. The old system was fork-based and used pkg_resources and multi-installed packages. The modern deployment is a simple, pip-installed process.
3) The code underwent other unrelated but substantial changes.

So although I thought I was on to something when I added the wrapper, suppressing the error, I was never able to detect it, and it seems to have gone away now. I was hoping this would shed more light on the problem and describe another use case, but at this point, that may not happen.

Unless the problem recurs in our application, or we have another application where the problem arises, I'll focus on the Python side as suggested by Amaury.