How do I disable Chrome's two-finger back/forward navigation?
I know its over a year later, but I had the same question, and then figured out the answer myself.

Open terminal and type:

defaults write com.google.Chrome AppleEnableSwipeNavigateWithScrolls -bool FALSE


Then restart Chrome.

Now you can have it enabled system wide, and just disabled for chrome. By the way, this works for any app, just replace com.google.Chrome with the bundle identifier of the target app. 

If your interested in how it works, the AppleEnableSwipeNavigateWithScrolls is the global setting, that can be overwritten for any specified app. 

Hope this helps someone in the future.