Bind and mydns can not be installed together. You will have to uninstall bind, it is not suppoerted by ispcomfig 3.
2) why is stopping the bind-service not mentioned in the INSTALL_DEBIAN_4.0.txt ?
because bind is not installed by default on a debian system, so there is nothing to stop. You should have followed just the ispconfog 3 installation guide without installing bind first!