If I’m not mistaken, the “ffmpeg-wrapper” project you linked to is out of date and not maintained. FFmpeg is a very active project, lot’s of changes and releases all the time.
You should look at the Xuggler project, this provides a Java API for what you want to do, and they have tight integration with FFmpeg.
http://www.xuggle.com/xuggler/
Should you choose to go down the Runtime.exec() path, this Red5 thread should be useful:
http://www.nabble.com/java-call-ffmpeg-ts15886850.html