I've been thinking about simplifying this in some way, but if you want to make a drag'n'drop script it'll be that much easier on me.
The terminal commands to do it are:
zip -X0 bookname.epub mimetype
zip -rX9 bookname.epub * -x mimetype
The first line makes the zip file (with epub extension) with only the mimetype and no compression (the -0 switch). The second line recursively goes through the directory (-r) and adds everything else (the *) to the zip file at maximum compression (-9) while excluding the mimetype file (-x). The -X switch ignores any extra file attributes.
It's not a bad idea to precede the whole thing with this command to clear out the .DS_Store files first:
find . -name '*.DS_Store' -type f -delete
(I have that aliased to 'rmds' in my .profile for typing simplicity.)