Peter White's web site claims that you can use the hub dynamo in place of the wheel magnet to provide data to your computer, which seems like a pretty elegant solution to the problem.

Considering how close I have to keep the wheel magnet to the sensor to get my bike computer to work, it should be pretty easy to mount the computer pieces far enough away from the hub generator to eliminate interference. I have a Schmidt hub generator on one bike and a Shimano 3N-71 hub generator on another bike, with computer sensors on the back wheels of each bike, and there's never been a problem.