Boosted Varnish for Drupal - what to do with "Control: no-cache" headers?
drupal_add_http_header() in your own module will allow you to override Drupal's headers.

Not that it's needed - your headers will only be set to no-cache when you hit Drupal directly. Not for boosted statics. It is a good thing. You want to keep HTML from boost in varnish, after all, not the one generated directly.

I'm proposing to leave it be. Files from Boost cache will not generate these headers, so will be cacheable for varnish. You will only skip caching pages generated on direct Drupal hits. But you want to skip them. They may contain messages, for example. Boost does not cache when there are errors and messages, so leaving no-cache in Drupal will let you to use this behavior and make varnish respect it.