Thanks for expressing your concern; this is definitely understandable!
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First of all, Leanpub just turned 11 years old, and we are established, stable and profitable. But it's always good to think of alternatives for a worst-case scenario.
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The closest alternative is to just have your Markua be considered Markdown (since Markua is a dialect of Markdown) and put it into a program which converts Markdown into PDF or EPUB.
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The best (in our opinion) open source program which does this is called pandoc -- it takes many formats (including multiple dialects of Markdown) as an input format, and it can produce many output formats including PDF or EPUB. The GitHub-Flavored Markdown (GFM) dialect of Markdown is the closest dialect of Markdown to Markua.
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Now, the result won't be ideal (since any Markua extensions to Markdown will not have the desired effect, and since Pandoc PDFs by default look different than Leanpub PDFs), but it will certainly be a start. After all, Markua is just Markdown plus some extensions. This is why the Markua specification is literally written as a fork of the CommonMark specification, with all the Markua extensions shown with (M) in their names, so that it is completely clear what parts of Markua are identical to Markdown, and what parts are extensions. The GitHub Flavored Markdown specification is also written as a fork of the CommonMark specification, so this is an established practice.

Finally, please note that you can write a Leanpub book using nothing but the parts of Markua which are identical to Markdown. After all, when we document the Markua needed to write a novel, it is 100% identical to every dialect of Markdown we've ever seen, going all the way back to John Gruber's original description of Markdown in 2004. (This is why you can drop a Markdown manuscript into Leanpub and click the Preview or Publish button and it just works...)