Why write markup for index.php?

WordPress might extend the existing template hierarchy in a future version. Your users would get a blank page after an upgrade. So write at least the basic loop, header, footer and pagination.

Another point: I use and see at the index.php usually as the default template. I treat its layout as the core concept and all other templates as specialized variations. Your theme will be easier to understand if you build a complete index.php that doesn’t look like a forgotten stepchild.