What we did for now, and are hoping to compile it into a plugin, is hook into the wpseo_metadesc filter (yes, the Yoast plugin is awesome) and do a bunch of fancy stuff. Inside there we check for post_type and then grab the custom field(s)we want and add to / update the description. What's really cool is that the admin side honors the filter, so the custom column in the post views will show your custom description.
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