It is possible that some website stil using iframe elements in his website such as Google Doc. However, there is a solution to fix this problem. This by changing the Zoom engine in the Zoom Safari extension Options page, from "web CSS zoom" (stylsheet) to the "built-in browser zoom" engine.
Just follow the steps here below to change the zoom engine:
1. Install the Zoom Safari extension back in your Safari web browser
Download Now for Safari™
2. First, open the Zoom for Safari app
3. Select from the app menu the item "Options"
4. You see the Zoom Safari extension Options page show up
5. Scroll a bit down until you see the topic "Zoom Engine", and enable the first radio button
6. And at last restart your web browser
What is the different from CSS and built-in zoom? The CSS zoom is more smoother in zooming in and out of a web page.