If you are going to speed up the entire video, this is easy to do in AviDemux. You should be aware that most people find AviDemux a bit flakey however.
There are only a few free non linear editors that most recommend. Lightworks is powerful, but not easy to learn. Aviutl (there is an English version at Videohelp.com) looks good, but there isn't much documentation, and not that many people using it. Kdenlive is reportedly very good for Linux users.
And you should ask at Videohelp.com for more answers. Those guys use Avisynth or Vdub most of the time, sometimes ffmpeg. I'm sure they could come up with some example scripts for you with Avisynth. I'm not comfortable with command line editing personally.
I did find one program that I'm not familiar with that might work for your particular need. It is called slomoVideo and can be used to slow down or speed up video. It is also available at Videohelp, though it is a very slow download. This program uses ffmpeg.