Sounds like you just need to train your colleagues to be a bit more disciplined with their package managing. It's not that hard to be clean about dependencies with conda. Maybe my take on it can inspire you here: https://haveagreatdata.com/posts/data-science-python-depende...
Re the extra "virtual environment", you can just use conda's base environment in prod. Here's how to do that: https://haveagreatdata.com/posts/step-by-step-docker-image-f...