I've never been able to. It maybe doesn't happen as often as it used to, but it's still pretty common for me to look at an issue with a customer and stumble upon folders with the (2) at the end of the name that just contain one document.

What I've done is schedule workflows to run prior to whenever these folders would get created, and create the folder with the scheduled workflow instead. If the folder already exists, it won't create the duplicate.

For example, I have a customer who stores documents in a \%Year\%Month\%Day\ structure. The %Day token would come from today's date, so every day, there's a workflow that creates the \%Day\ folder for the next day. The duplicate folder never appears when doing it this way.