Sounds like you are in a fairly new version of windows? Maybe XP?
You should be able to just kill the process...
taskkill /IM vlc.exe
Details are found here on various ways to kill the process...
http://www.tech-recipes.com/rx/446/xp_k ... _taskkill/
You can shut down gracefully, you can force it... I think it shoud work from any command prompt. Now if you are just looking to "pause" the video and then re-start it... that's a different story.
In our application we have a batch file that runs in the scheduler at 7pm and stops the video from playing... then at 7am another batch file starts the player in full screen mode running a video playlist. We do this in XP.
Good luck.