As a Python developer and ebook writer I've gone a similar route. I'm currently writing in emacs using reStructuredText as my base format and have written code to generate  clean epubs which translate to mobi/kf8 pretty well. Part of this is a CSS file I'm working on  to make common formatting "just work" across the big ebook readers (old-kindles, newer kindles, ipads, nook and kobo).
I've spent a little bit of time (and money) getting very nice pdf generation working using sphinx and the memoir class for latex. It's not there yet as I've been focusing on the ebooks.
Yes, it feels like you need to be a programmer to create ebooks right now. You definitely need to feel comfortable editing html and css. I'm not completely happy with rst as the base format, but I don't think there is another lightweight markup language specifically targeted to authoring books. Even sphinx which is supposed to be for documentation isn't really well suited towards books. So there's little hacks here and there. Plus as I usually write about Python related material, rst lets me "test" my books using doctest and I can even templatize some stuff (I'm doing that in a book I'm currently working on).
0 - https://github.com/mattharrison/rst2epub2
1 - https://github.com/mattharrison/epub-css-starter-kit