Subdirectories versus Subdomains

I would like to install WPMU with subdirectories on an existing website with 6,500 posts, however I see this remark for WPMU:

"If you have had WordPress installed for longer than a month and are attempting to activate the network, you will be told to use Sub-domain sites. This is in order to ensure you don't have conflicts between pages (i.e. ) and sites (i.e. ). If you are confident you will not have this issue, then you can change this after you finish the initial setup."

Is there a workaround - solution?