Quick workaround (at least it works for me):
Edit /usr/share/thumbnailers/atril.thumbnailer as root, move to the last line (which starts with MimeType=) and remove the last part of it - application/epub+zip;.
The line should end with application/vnd.ms-xpsdocument; after that.
Log out and log in back. Now atril-thumbnailer should not be invoked on epub files.