Oooh I'm going to let Mike handle this but I'd just like to say yes this is exactly something you should use JBMS for. We'll certainly be extra helpful if you'd like to work with us. (we get early adoption and better requirements definition in the mail based applications space). Mike's been refactoring things to make this more possible so I'll let the tech explanation come from him on that..
Yes, I am currently do some refactoring. However I am trying to make sure that the fundamental architecture remains intact. Your best bet is to use a mail listener placed in the local delivery chain. The listener would simply check the to address (or subject or whatever criteria you are interested in) and push the context of the mail onto you workflow system. I think (but have to check) if you return null from the listener then the chain will stop delivery at that point. Andy could you confirm this?
I would also at some point like to open up the routing portion of the mail delivery such that you could plugin listeners and different routing rules there also.