Solution 1:

looks like this answer related to a similar problem might do the trick: https://stackoverflow.com/a/20692071/620141

in short:

  1. Edit ~/Library/Preferences/com.apple.symbolichotkeys.plist (you can use Xcode).
  2. Find the code for kCGHotKeyLookUpWordInDictionary (70), and set 'enabled' to OFF (if it's not there just create an entry '70' with 'enabled' = OFF).
  3. Restart your system

EDIT: In your case, it should be:

Key Down
    Characters: ,
    Unicode:        44 / 0x2c
    Keys:       ⌘,
    Key Code:   43 / 0x2b
    Modifiers:  1048848 / 0x100110

so you should be using key code 43 with modifier 1048848

Extra help:

  • answer's source & extra guidance
  • Tool to find the key code (older macs only)
  • Alternative tool that works on Yosemite (Apple Store, free)

Solution 2:

System Preferences > Keyboard > Shortcuts > App shortcuts > +

Title it "Preferences..." and remap it to CommandAlt+, and voila, you can now use Command, in Google Docs.