You may wish to avoid using iBooks Author (iBA) and the iTunes store for distribution since what you seek to do (provide a free download to paying customers that pay elsewhere) violates Apple's guidelines that each SKU either be paid (and paid through an AppleID and Apple's payment system) or free to all who wish to download it.
There is nothing preventing you from controlling the distribution of a generic source file that's PDF or ePub format and using whatever payment system you want. Also, as long as your work is free - you can use iBA even distribute PDF/ibooks files outside the App Store ecosystem. In both these cases, your customers would then be free to choose to consume your work using iBooks or other apps as they choose. You will be bypassing Apple's DRM, review, code-signing and customer handling (billing, first level support, account setup, etc…) so there seems to be little avenue you will have to control each person from re-sharing your work and you'll probably need to spend significant energy and time to implement a framework from which you build your multimedia ePub book if you choose to go without the iBooks Author packaging and authoring system.
You should be in the clear to use iBooks Author to craft your paid book for distribution through Apple's channels and reevaluate whether you need to somehow offer those books for free rather than gifting them. You might need a lawyer or to work with Apple to determine what modifications would be needed for you to have a paid work for sale and a free work for distribution to your paying customers. I would guess you would be in violation of the license terms of iBooks Author if you were selling one version and made a second version that had trivial changes and was distributed outside the store to get around the pricing intentions Apple has established.