You are the editor. It's your job to make something that is easy to follow and understand. Edit audio as needed so it is clear and concise. Leaving pauses where needed to comprehend what is being demonstrated on the screen or for someone who might be watching and taking notes. Don't make the pauses too long or you will loose some people, it's a tricky balance. Also, taking out the ums, clicks, and pops makes it a more professional product.
With instructional videos you will obtain better retention value if you give the viewer the key points in all three ways; show them the action you are talking about for their eyes to see, label it with text on screen for their brain to read, and have it described in the voice over for their ears to hear.