Where do you think the theme is hard wired in the UserEJB? I can't see one.
In the Nukes Core module, you can set the DefaultTheme attribute to be what you want. If you want people to only have that theme, then you can not deploy the Theme module, and change the YourAccount module to not allow a theme to be selected.
.... or just have only one theme installed. That way you do not have to change the YourAccount module.
Take a look in the ejbCreate. I wanted to set 'imagic' as the default for new users(which is set in the core module as you mentioned - I did think this was just for first time users rather than the whole site though?), however I noticed that if I created a test user through the register function then their initial theme is set to 'seabreeze'. This then set me off on the witch hunt to find out why..hence UserEJB - I have taken a recent snapshot(not straight from the repository though), so not sure if it has been sorted in the last few days...