You can safely delete the whole ~/.wine folder. PlayOnLinux, as you guessed, is self-contained. Yes, you do need Wine installed, but you don't need that ~/.wine folder.
NOTE: If you have game-save files in ~/.wine, then back them up. If you don't, you can just delete it.
PS-Since /home is NFS mounted, I moved .PlayOnlinux to a location on the local disk and created a symlink to it. It seems to work fine, but it would be nice if the initial setup had an option to do that or otherwise put the PlayOnLinux dir someplace else -- at least a dialog saying it needs this directory and let you create it manually (so you could do above before filling it up).
Not everyone has that set up (actually, it is not extremely common), and would probably cause more issues. Of course, for advanced users, that method works fine, but it is not common enough, IMO, to have the function integrated in, especially when you can simply do what you did; copy and make a symlink. :)
