If/When you get this error:

It seems like uTorrent is already running, but not responding. Please close all uTorrent processes and try again.

you could simply kill all the utorrent processes with:

killall -9 uTorrent.exe

Then just open utorrent, not the installer.

You can also open µtorrent with '/NOINSTALL' parameter but then you can't change any settings (if I understood right). E.g.:

C:\Program Files\uTorrent\uTorrent.exe" /NOINSTALL

#!/bin/sh
QUICKPARLOCATION="c:\\Program Files\\uTorrent\\uTorrent.exe"
if [ $# -eq 0 ]; then
  wine "$QUICKPARLOCATION"
else
  PARAM=`winepath -w "$*"`
  wine "$QUICKPARLOCATION" "$PARAM"
fi