It is likely not possible to change in camera. For power and efficiency reasons, cameras generally use dedicated encoder hardware to encode the video in real time (this is why your camera can encode h.264 video live, but when you try to encode it on your PC, it takes longer, even though your computer is far FAR more powerful.) The caveat of this is that there are a limited number of options for how it can store the file.
Many Canon cameras record as an h.264 stream embedded in a MOV file. While this isn't super convenient in your case, it also isn't the end of the world. MOV and AVI are both simply container formats. They store a particular type of stream within them that is based on a codec. Since both MOV and AVI support an h.264 stream, you should be able to use a software package of your choice to take the h.264 stream out of an MOV container and store it in an AVI container and then your software should work fine with it.
I believe that QuickTime Pro offers a Save As option that will go to m4v or mp4 (which is more of a raw h.264 stream) if your editor supports either of those options. It might support Save As an AVI as well, but my memory is a bit fussy on that since I haven't had to do such conversions in a while. (My editing software supports both.) There are literally any number of other tools (including free ones) that can do the same thing as well.