As @MoifMurphy mentions in the comments, the free and open-source VirtualDub is definitely capable of joining videos. Editing in VirtualDub is explained here in detail, as well as here, but basically, you need to:
- Open the first file
- Select File » Append Video Segment, do this repeatedly for all videos you want to append
- Select Video » Direct Stream Copy and Audio » Direct Stream Copy. This is important so that your video isn't re-encoded.
- Save the file as AVI.
- Windows Movie Maker should be able to read it.
See the VirtualDub documentation for more info.
Camera Raw pictures are going to be hard to import to a video editing program. They were never meant to read those files, and you'll need to convert them before making a time lapse video.
Professional software like Adobe Lightroom or Photoshop will assist you in doing so, while also performing tonal correction on the images. This is almost inevitable, since the Camera Raw files are, well, raw data, never meant to look "good" out of the box.
I guess IrfanView can read CR2 files and also batch convert them to, let's say, JPEGs. You can then import those. If you need to edit the files before creating the video (i.e. adjust tones, brightness, etc.), you can probably do this very efficiently with Picasa.