I found link here: http://wiki.wesnoth.org/MultiplayerserverWML
This describes handshake, login, chat commands.
The issue you raise is you cant pm offline players. This chat bot idea is by far the simplest solution, otherwise you will be rewriting the chat interface in C++. Also, implenting new special chat features on server-side. Currently one of the design criteria is that the server does as little work as possible, because operating it costs money. Maybe the devs will like your idea but I would bet against it. I would be willing to help implement a chat bot, I doubt it would take more than a day or two.
Edit: Keep in mind, this idea may sound very simple, but if you change the client server contract you will have to rigorously test the new server which is a huge job. Right now the server is extremely stable; this feature is definitely not worth it if it means even a few days of server down time from an unexpected bug in implementation which caused games or chats to be dropped etc. The server is already pretty complex and pretty old. There's no risk of any of that with a chat bot.