I'd like to suggest that Pandoc allow attributes to be attached to any Markdown element, not just code blocks. So for example, if it encountered this:

#{.main} Header

it would generate this:

<h1 class="main" id="header">Header</h1>

rather than this:

<h1 id="main-header">{.main} Header</h1>

Ditto for, say:

Header
----{.main}

...which is probably even legible enough to fit with Markdown's philosophical aversion to looking, well, marked-up.