in 12.10 there was a tab on preferences of empathy that i could configure notifications in empathy and now in 13.04 it's not available anymore
so is there any way to disable the notifications or the balloons ??
You can disable using dconf editor.
Go to:
org > gnome > empathy > notifications
and disable the keys "notifications-enable" and "notifications-focus". It worked to me in Ubuntu 13.04.