If you want to be friendly to your users, generate encrypted .epub format and not .pdf.
pdf is great for its original purpose of print preparation, but terrible for more flexible formats.
As different ereaders have different screen sizes and resolutions, and different people will want to read with different font sizes (**),
pdf format will be very hostile in all cases except the one that excactly fits how you make the pdf.
I think that InDesgin will create encrypted epub or pdf files for you.
For the encryption to be effective for your purposes you need to encrypt differently for different AdobeIDs.
Looks as if Adobe's official way to do that is Adobe Content Server.
I suspect the cost of all that adds up quite a bit; you may want to look at third party solutions that handle all the infrastructure for you.
(**) or even the same person: I change font sizes depending how tired I am.