What is Application Loader and why does it want to open EPUB?
Application Loader is the app used to publish content you've created on the App Store. In addition to actual Apps, this also includes ebooks in EPUB format. It's part of Xcode and no, it can't display EPUB documents, so you may want to tell OS X to always open your EPUB documents with Stanza again (this association likely got overwritten when Xcode was last updated).