Same situation I am in with one of my sites. I have Zero pages indexed according to Google's Webmaster tool but still get a good amount of traffic from them. Google does not show any backlinks in the webmaster tool since the unnatural links warning came several months ago.
The problem is, I have not bought or exchanged any links. All my links are natural. Seriously, isn't it the business of Google to discount any links they think are bad? What if someone gets spammed with hundred or even thousands of spammy links. That's a lot of work to update a disavow list. Unbelievable from Google that.
What's more excruciating is that you always get the feeling each reconsideration request will be met with the same, what seems like an automated message, that unnatural links still remain. Unbelievable. Google really does have too much power. Its almost as if they play around with peoples livelihood.