Homebrew says my Python installation could cause issues and I'm not sure what to do
When I run brew doctor the first bit of output says this:

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!


Followed by a warning similar to yours about config files that brew can see which are part of an Anaconda Python install.  So, if you're not having any problems, you shouldn't feel too bad about taking their advice and just ignoring the warning.

However, the reason that you're getting the warnings is because the MacPython install process added a symlink in /usr/local/bin/ to it's Python directory under /Library/Frameworks/....  There's nothing wrong with this per se, but, as you've found, it's always possible that it could conflict with assumptions made by other stuff that uses /usr/local/bin/ (e.g., Homebrew).

You might want to look into virtualenv as a way of managing your Python development environments in general.  I haven't given this much thought, but I'd be tempted to remove those links that MacPython put in /usr/local/bin/ and create a virtualenv that points to whichever MacPython version you want to use for a particular project.