Current implementation of "Edit Online" assumes the user will create a new version when they close MS Office. For instance, "Edit Online" a word document. The document library will automatically checkout the document (*.doc and *.docx) and then MS Word will open the file. When the user closes word, their file will be automatically checked in and a new version created for the document.
Users should be given a choice to manually checkin the file. Thus, the DL does not automatically checkin the file when MS Word exits.