Disable Cmd + , in Safari
looks like this answer related to a similar problem might do the trick:
https://stackoverflow.com/a/20692071/620141

in short:


Edit ~/Library/Preferences/com.apple.symbolichotkeys.plist (you can use Xcode).
Find the code for kCGHotKeyLookUpWordInDictionary (70), and set 'enabled' to OFF (if it's not there just create an entry '70' with 'enabled' = OFF).
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 &amp; extra guidance
Tool to find the key code (older macs only)
Alternative tool that works on Yosemite (Apple Store, free)