It depends on what the underlying format (aka codec) being used is.
Many digital still cameras record video in "Motion JPEG" (or M-JPEG) with "PCM" audio. This means they are just recording a series of JPEG pictures (as that's what still cameras like to create,) and calling it a movie; and throwing in uncompressed audio. (Think CD Audio, only at generally lower quality.)
AVI and MOV are just 'containers' (as you figured out,) both of which can hold M-JPEG with PCM. So converting from one to the other should be simple in QTPro. Just export M-JPEG with PCM, and you should be good. QTPro should keep the actual data in its native format without losing any quality, only changing the container.
Heck, some digital cams use so little of the 'container' information that just renaming the file from .avi to .mov will make QuickTime use it just fine.