My choice would be for it to act like when I open a PDF and a dialog box comes up with open with... and save to.
I have been downloading a number of epubs off of archive and they are not ready to use. I will need to use sigil and notepad ++ to civilize them. So a dialog box that had open with as the default option and save as the second option would be my choice.
If it were configurable that would be the best of all. That would allow current behavior which is great for ready to read epubs and the behavior which I mentioned which would be more useful for those downloading epubs that need work.