I found Kotobee, which has a free Author application. With this application you can make interactive ebooks for epub, kindle and many other formats.
I am also writing stories and was looking for making ebooks interactive. In my free time I looked for a solution where I could integrate the html5 Construct 2 interactive projects with an easy ebook creation. I am not far enough in the process but use the strong features of each package (Scirra for the actual interactivity creation and Kotobee for the creation of the ebook) will provide you with the interactive ebook you are looking for.
I am sure when I think about it, that you can create the whole ebook with Construct 2 but you have to do more things yourself.
I was happily surprised to find this flip ebook thread started somewhere in 2013. This proves again the powerfull versability of Construct 2!!!