As promised I am publishing script that will close Zune and start WPConnect automatically. I have placed this script on my desktop and I start it each time I connect my Windows Phone to computer. Please find script in next part of post.

ECHO (c) Michal Jankowski 2012

SET %errorlevel% = 0
SET /a counter = 0

taskkill /IM zune.exe
IF %errorlevel% NEQ 0 (
  GOTO End

ECHO Closing Zune...
PING -n 1 -w 5000 >NUL


  "%ProgramFiles%\Microsoft SDKs\Windows Phone\v7.1\Tools\WPConnect\x86\WPConnect.exe"
) ELSE "%ProgramFiles(x86)%\Microsoft SDKs\Windows Phone\v7.1\Tools\WPConnect\x64\WPConnect.exe"

IF %errorlevel% == 0 (
  GOTO End
) ELSE (

  IF %counter% GEQ 2 (
    ECHO WPConnect can not be started...
    GOTO End

  ECHO Retrying in 5 seconds...
  PING -n 1 -w 5000 > NUL
  SET /a counter=counter+1

  GOTO ConnectToPhone


And whole in file: