This is already possible through the onMessageToOperator and onMessageToVisitor hooks in the Olark JS API (https://www.olark.com/api). I'm excited to see what people will do. :)

Olark is actually entirely done over XMPP, so you could theoretically connect directly to Olark with any standard XMPP client. Trillian is doing some cool stuff in their latest Mac OSX beta using some of our XMPP extensions.