HI Mikhail,
This is a great time for you to get involved in evolving what we have. As far as I know due time limitations we will not be able to provide the features that you want for 6.0, maybe for 6.1.
We should be able, with the help of community members like you to evolve what is being provided out of the box in jbpm6 to provide more advanced features.
As far as I understood for your email you want to deploy your app in Tomcat, and at the same time you wanted to have all the features provided by a EE container such as JBoss which is ready for more enterprise things like handling XA resources and transaction components such as MDBs. Nowadays JBoss is extremelily modular, so you can enable the web profile plus all the other components that you need and disable all the ones that you don't. I will always recommed to go with JMS if transactions are heavly involved in your scenario.
I guess that we can find a way to remove the dependency to MDBs if that's what you need, but you will need to solve in some other ways the features provided by such components.
Cheers