Merging epubs directly would be problematic. Which <title> metadata should take precedence for the final epub? How about <author>? I'm not sure how you could solve this.
On the other hand, merging epub file contents is something you can do easily with Sigil today. Let's say you have epub A open in Sigil, and you want to merge it with the contents of epub B. Simply unzip epub B and in the Book Browser select "Add existing items" and select all the XHTML files from epub B. This will alsopick up all the CSS and image files that those XHTMLs reference. The epub B XHTMLs will be appended after the epub A XHTMLs in the Text folder.
Presto, contents merged.