If you do not want to launch Total War: Shogun 2 through the STEAM client you can create a desktop shortcut as specificied below:
- Open Steam
- Click on Games
- Click on View Games Library from the drop down menu
- Right Click on Total War: Shogun 2
- Select Create desktop shortcut
- Steam will provide notification of the shortcut
- Click Ok.
- Exit STEAM
Total War: Shogun 2 can now be launched from the desktop.