Sounds like a good candidate for an Import plugin.
But you could also use a pre-commit hook to wipe the working tree and extract the EPUB:
Code:
git ls-tree --name-only -z HEAD | grep -zvE "*.epub$" | xargs -0 rm -r
unzip -qqo *.epub
git add .
Then a git commit will fetch and commit any changes from the EPUB.
Sigil includes a feature to save files outside Sigil, open them in an external editor, and read back changes.
You could also make use of calibre's Unpack/Explode Book (available through the CLI as `calibre-debug -x /path/to/ebook`).