Apple has strong policies to weed out low-quality or abandoned apps from its store. To enforce this, Apple requires apps to function well on newer devices, so if a developer doesn't update an app to work with newer standards (for example, screen size/resolution), it is removed. At a certain point, my guess is that Gospel Library 2.5 stopped meeting Apple's standards and also could not be updated, so it was removed.
The situation is a little different for your Kindle app (or other apps) because Gospel Library 3 was released as if it were a different app from Gospel Library 2.5 – so both Gospel Library 2.5 and Gospel Library 3 were listed in the store for a time – probably for this very reason, so people with older devices could download the old version (the new version having new features that weren't compatible with older devices).
Gospel Library 3 was released in June 2013. Apple started allowing people to download the "last compatible versions" of apps (like you can with the Kindle app) in September 2013. Had Gospel Library 3 been released after September 2013, most likely it would be available in the same way the Kindle app is.
Samuel Bradshaw • If you desire to serve God, you are called to the work.