"from the looks of your response it seems that you are settled on the idea of tying the entire thing to Empathy/Telepathy"
Not sure how you read that between the lines, especially since I prefer Pidgin to Empathy ;)
If we need to be able to tell which chat application the user prefers, we may just have to ask the user! We do it for web browsers so we know what app to open when you click on links; seems perfectly reasonable to ask what your preferred chat app is to make sure we're launching the correct application on behalf of the user. This is a lot of work, though.