Well, I obviously don’t know enough about this subject. There are so many codecs and containers (mov is just a container as is avi) that it’s hard to keep up. You are going to lose quality with any conversion, that’s just the nature of the beast. I still suggest giving Mpegstreamclip a try, some Mac users I know like it along with Avidemux. Another option is Format Factory, http://www.formatoz.com/, it has a pretty simple interface, just choose Video and then all to Avi or Wmv. There are several settings you can adjust, maybe too many, so feel free to play around with them.
It seems strange the Movie Maker won’t import mov files but I don’t think iMovie does either.
Oh, you probably need Quicktime installed on your PC for Mpegstreamclip, you might already have it. Sorry I can’t be of more help but MovieMaker and mov files are not something I use. One other thing, how are you getting your movies from your camera to your hard drive?
One other thing to try just for kicks is VLC, if it can play the mov file it can convert it to wmv or avi. It might even be able to capture the video directly from your camera.