When in this Answer says "org > gnome > empathy > notifications" it means the schema in dconf-editor.
Disable Empathy notifications With Dconf-Editor
Make sure you have dconf-tool installed.
1) Open a Terminal window and type:
sudo apt-get install dconf-tools
2) Go to the dash home and search for the "dconf-editor" to open it
3) Navigate to the org.gnome.empathy.notifications and uncheck the key "notifications-enabled"
Disable Empathy notifications With gsettings command
If you prefer... you can do it with one command.
1) Open a Terminal window and just type:
gsettings set org.gnome.Empathy.notifications notifications-enabled false
Hope it helps.