I have a 2 classes which implement a common interface.

Class A implements MyInterface {
}

Class B implements MyInterface {
}

How can I use the same XML configuration file for DB operations on both classes, or can the XML file refer to the interface?

Just map the interface with the two classes as subclasses. Look at http://www.hibernate.org/hib_docs/reference/html/inheritance.html

But if I want generate class that have to implement some interface (without mapping). Generated code must contain code only.

And sometimes I need to inherit from abstract class as parent class with default implemented logic (instead interface).