I'll be shooting a juggler against a green screen. Will the motion of the balls present a problem during the chroma key?

yes and no. Interlaced DV video is tough for chroma keying, but not impossible. I can be done, sure but the results are going to be hit and miss. Stay as far away from the Greenscreen as possible (8 feet is usually good) so there isn't as much green spill on the actor. What is your shutter speed? Are you going for a blur or a high shutter speed as in Saving Private Ryan without much blur?

The motion of the balls can present a problem for you because of the motion blur. Where there's motion blur, your video signal will have a mix of foreground + background and it's difficult to tell the exact combination.

One solution is to use a very fast shutter speed to reduce motion blur. You'll need a lot of light!