Just my opinion, but I think your best bet is to put all content in the database right away, but not publish it to web. Instead, attach the content to a given issue and you could output a .epub format pretty easily, and both iPads and Kindles like .epub (or did last time I checked).
Pull the content for the reader (maybe via json) and you're home free.
Plus, the content is already in the database when you want to publish it to the web site at some future point. .epub is pretty simple, and the whole thing could run off what you have already. Trickiest part would probably be restricting access, but that could be done, too. Note that I'm talking about the .epub format, not the Flash "Epubs" roaming around, which are usability nightmares and don't solve any e-reader problems anyway.
On a side note, if the new site font size could be bumped up a hair, old eyes would appreciate it.