We are looking at immersive storytelling and initially our Editor was against that, as he said that there is a contract between you and the reader to maintain the world you’ve created and that clicking on links breaks that contract, as you take them out of that storyworld. However, I like to think that such immersive processes take us deeper INTO the story and not out of it.
Just my opinion, but good linking enhances my experience of a story. I see it best used in online journalism (including with multimedia) where links allow, say, a documentary film to be extensively sourced. You see it a lot in museum apps, too.
For uses within a specific story, interactive fiction does this well. Tools like Twine and Ren'Py are bit more niche, but allow the user to control the flow of text on the page using some pretty basic CSS and javascript. Some of them are not that far off what it sounds like you're trying to do (as far as I can tell).
Speaking from a games perspective, a lot of the immersiveness of the experience comes down to how the story both excites and involves the reader. So really not that far off old-fashioned good writing: pacing, tension, conflict. But you can use the links to let your user move deeper into different aspects the story you're creating, even take on a degree of agency in what subjects/sources/scenes she reads. Giving up that level of control takes a lot of trust, but can really pay off.
This sounds like an interesting idea, and I know a couple people who have released e-books this way and found it a useful way to let an audience explore a (sometimes niche) subject. Sadly, I can't really give you any opinions on iBooks, but looks like others can.
