There was a time, when I was so fed up of the Calibre being so bloated, while all I needed was just a convert capabilities, that I started to rip off parts of the Calibre, clean it up, make things simpler, removing unnecessary things and trying to understand what is happening behind the conversion, resulting with ebook-converter[1], which simply do the conversion, without all the management/downloading rss/editing/what have you. It is usable right now, but I'd say it's still somewhere in between alpha and beta stage. You could give it a shot.
[1] https://github.com/gryf/ebook-converter