It's certainly not related to the macOS Sierra update. I've had this issue since I started using this MacBook Pro and a Magic Mouse in 2012. I eventually got used to it and avoided scrolling with the touchpad and mouse. Occasionally though, I still accidentally scroll when I click and a few of those times I placed a bucket of lava, which killed me and destroyed things.
It actually isn't related to Mac at all. Most mice have a wheel that triggers the scroll event every "click". Other mice such as the Apple Magic Mouse, Microsoft Arc Touch Mouse, etc. trigger the scroll event every time you move the finger the slightest amount.
I've also tested this on Arch Linux (with XFCE). By default, the Magic Mouse scrolling is painfully slow in pretty much every program, but works great in Minecraft. I typed the following commands to set the scrolling sensitivity to a comfortable speed:
sudo rmmod hid_magicmouse
# scroll-speed value from 0 (slow) to 63 (fast):
sudo modprobe hid_magicmouse scroll-speed=40 scroll-acceleration=1
This made scrolling work great in every program except Minecraft. This isn't as much of a problem on Linux since you can easily create a shell script to toggle the scrolling speed. On macOS and Windows, changing the scrolling speed every time you run (and quit) Minecraft is NOT a good solution. A good solution is to implement a scrolling sensitivity slider in the controls menu.
That probably won't do anything because I had this problem in 1.4.6 as well. I am using Magic Launcher and Modloader, ReiMinimap, Biosphere, and Optifine. Maybe it is the mods that cause this problem then.
I have 7 on the list. It does it with any number of servers.
@Seth It isn't just an Apple issue. As I have said before, it also happens with other operating systems.
The driver program detects when you move your finger on the mouse and sends scroll events. When you change the sensitivity, it basically changes how often it sends scroll events. A mouse with a scroll wheel will trigger the event on every "click". I've noticed that some modern scroll wheel mice also have smooth scrolling and don't "click" when you turn the wheel. Apple has likely changed something in the code that handles scrolling, which is why it is happening more consistently in macOS Sierra.
Afaik the reason Minecraft is so sensitive to mice with smooth scrolling is because it is switching hotbar item on every scroll event. Changing the scrolling sensitivity in your mouse settings is not a proper solution. Minecraft should implement a scrolling sensitivity slider. 100% = default (i.e. how it current handles scrolling), 75% = 25% of scroll events are ignored, 50% = half of scroll events are ignored, etc. 0% would completely disable scrolling for the hotbar. As @Trejkaz suggested, being able to rebind the next/previous slot controls is also a nice solution.
An alternative, less ideal solution is to use a program that, when Minecraft is the active application, either:
a) Changes the scrolling sensitivity (only for Minecraft) or
b) Disables scrolling and binds other buttons to scroll up/down e.g. mouse button 4 and 5 (for mice with extra buttons)