Keynote 6.6.2, iMac, OS El Capitan: How do I export Keynote presentation to quicktime without the voice over?
I have two solutions, the first one is to export to QuickTime with the audio and then remove the audio the secondary is to first remove the audio then export to QuickTime.

Solution 1 
First export to QuickTime 
Open iMovie and create a new movie project (you can remove the new project later)
Drag and drop the video file to the large grey section at the bottom
Right click and click Detach audio
Right click on the new green bar below and click Delete (all audio has been removed)
To export, Click File->Share->File and click next and save it where you will find it.

Note, this solution removes all the audio. If you would like to keep some, you can simply add the audio just before you export the file in iMovie by drawing it to the large grey section. 

Solution 2 
An audio file in a keynote looks like this:

They are placed on the slides and don't have any fixed positions so they can be located at anywhere. To remove them you have to look thru all the slides and remove them one by one. Click on it then press backspace to remove it.