It's not an iBooks issue - it is a file issue. You're talking about a file (.ibooks) you can't control once it leaves your computer. There are many applications that output unsecure files.
You could output a PDF via iBA and then lock it with a password given the proper utility, but you would lose all the iBA functionality and security would be based more on trust that the password was not being circulated along with that file. Same as if you zipped the .ibooks file and locked it with a password.
You want to control distribution, not the file contents. That approach goes beyond iBA, Pages, Keynote , Preview, Safari, etc. It's up to you at that point, not the application used to generate the file. Put the .ibooks file on your server, behind a password/logon and ask your trainees to not distribute.
You can put a password on an .iba file, but that file won't work on iOS/iPad.
As always, feel free to use the 'Provide iBooks Author Feedback' menu item for features you'd like added in the future, etc.
http://www.apple.com/feedback/ibooks-author.html