There is a way to make it work, it's requires a bit of work though!
Step 1:
Record the Prezi presentation using a screenrecording program (such as iShowU). Just keep pressing the arrow to go to the next slide but leave it at each slide for a couple of seconds. This way each slide will be visible for a couple of seconds before it changes to the next.
Step 2:
Upload your recording to YouTube.com
Step 3:
Download the YouTube video so you can import it into Keynote.
Step 4:
If your Prezi slide has 10 different slides, make 10 slides in Keynote. Import the YouTube video to each slide.
Step 5:
Now comes the tricky part...
Go to the first slide of your Keynote presentation and let the Prezi video play. Write down the time it starts and when the first full slide is visible. Then use Inspector (in Keynote) to let the video play from the time the Prezi video starts until the full slide is visible. This way the video will only play from the start until the full Prezi slide is visible in the video.
Step 6:
Now go to the second slide in Keynote and use Inspector to have to Prezi video start at the same time the Prezi video in the first Keynote slide stops. Let the video play until the second slide is fully visible and then use Inspector to have the video stop at that precise time.
Step 7:
Do the same for Keynote slide number 3; Use Inspector to start the video at the same time the video stopped playing in the previous Keynote slide, and let it play until the full slide is visible.
Example:
Keynote slide 1
The downloaded Prezi video from YouTube plays from 0:00 to 0:20
Keynote slide 2
The downloaded Prezi from YouTube video plays from 0:20 to 0:50
Keynote slide 3
The downloaded Prezi from YouTube video plays from 0:50 to 1:20
All you have to do in Keynote, is make sure the transitions between slides are as fast as possible so you don't see the transition between slides and make sure the video starts playing when you go to the next Keynote slide.
If you've done it correctly, you will start with the first Keynote slide showing the first transition of the Prezi video. Take all the time you want to talk and when you're done, just go to the next Keynote slide. The video will begin to play, showing you the cool effects you can use in Prezi, and when the full slide is visible, you can start talking. Done talking? Go to the next Keynote slide and the video will start to play.... etc etc etc!
Hope this helps!!