The keybindings in the chat window are not assignable by .gtkrc.  I have attempted a patch to make them work, and while I think it's pretty close, it's not quite there.  I'm not familiar enough with GTK to understand why.  Here's the patch:

--- empathy-2.25.92.orig/libempathy-gtk/empathy-chat.c
+++ empathy-2.25.92/libempathy-gtk/empathy-chat.c
@@ -707,6 +707,7 @@
              return TRUE;    
      }
 
+#if 0
      /* Catch enter but not ctrl/shift-enter */
      if (IS_ENTER (event->keyval) &&
          !(event->state & (GDK_SHIFT_MASK | GDK_CONTROL_MASK))) {
@@ -727,6 +728,7 @@
              chat_input_text_view_send (chat);
              return TRUE;
      }
+#endif
 
      text_view_sw = gtk_widget_get_parent (GTK_WIDGET (chat->view));
 
@@ -1275,6 +1277,7 @@
      GList           *list = NULL; 
      gchar           *filename;
      GtkTextBuffer   *buffer;
+     GtkBindingSet   *binding_set;
 
      filename = empathy_file_lookup ("empathy-chat.glade",
                                      "libempathy-gtk");
@@ -1311,6 +1314,7 @@
                                            "left-margin", 2,
                                            "wrap-mode", GTK_WRAP_WORD_CHAR,
                                            NULL);
+     gtk_widget_set_name(chat->input_text_view, "empathy_input_text_view");
      g_signal_connect (chat->input_text_view, "key-press-event",
                        G_CALLBACK (chat_input_key_press_event_cb),
                        chat);
@@ -1323,6 +1327,11 @@
      g_signal_connect (chat->input_text_view, "populate-popup",
                        G_CALLBACK (chat_input_populate_popup_cb),
                        chat);
+     g_signal_connect (chat->input_text_view, "message_send",
+                       G_CALLBACK (chat_input_text_view_send),
+                       chat);
+     binding_set = gtk_binding_set_by_class ((G_OBJECT_GET_CLASS(G_OBJECT(chat->input_text_view))));
+     gtk_binding_entry_add_signal (binding_set, GDK_KP_Enter, 0, "message_send", 0);
      buffer = gtk_text_view_get_buffer (GTK_TEXT_VIEW (chat->input_text_view));
      g_signal_connect (buffer, "changed",
                        G_CALLBACK (chat_input_text_buffer_changed_cb),

Probably this use of keybindings needs to be expanded to other aspects of empathy, but I don't know of any specific examples off the top of my head.