It looks like you have installed Python using another method before.
Don't be scared. Homebrew is engineered so it won't mess up your system
like Mac Ports et al.
You can always do
brew link --overwrite --dry-run python to
see first what exactly will be overwritten, without actually doing it.
If once you do this it look like it is only overwriting or deleting
*.py scripts, then you should be even less scared.