Ok here is my solution that worked for me:
Step 1: Go to MSConfig.exe (if due to some issue your system is not starting you can do the same from safe mode)
Step 2: Navigate to Startup tab and uncheck AiChargerPlus Application. I targeted to uncheck anything relevant to ASUS or AI Suite.
Step 3: Restart the system.(In my case my system just displayed the error message and could not login to windows, by doing this I was able to go into my system)
Step 4: Try to install AI Suite again using either installer or the CD provided. Navigate to Utilities>>ASUS AI Suite II, click next to move to next screen.
Step 5: The next screen will show list of ASUS Utilitites. Select TURBOV EVO and install it. (Yes its already installed and it will probably overwrite the existing files or whatever, but it worked for me)
Step 6: Now try starting AI Suite II, it should work. Change back to the default setting in MSConfig.exe and restart it.
I was able to login to my system, then start AI Suite II. Although I did not try to uninstall AI Suite II but the uninstall.exe worked and it displayed the expected window.