As long as links are not broken and resources are not returning 404 errors, my understanding is that it is not affected at all. The only thing I would make sure of is that fetch as google returns the page looking like it should. Here is a video from the authority on the matter.

https://www.youtube.com/watch?v=j3KgrbiB1pc#t=52

This might help, http://moz.com/blog/parasite-hosting-now-dominating-spam-results

Do you think it will help your site? Google says not to pay for links, but this is pretty much the standard of how online journalism works these days.

You are going to have to add a manual rewrite rule to the htaccess, preferably at the top. This might help, http://stackoverflow.com/questions/1321123/redirect-from-subdomain-to-domain-htaccess  But like Travis said, be careful, make a back up, because you can break your site doing this.

Jon,

I have never done it with a robots.txt, one easy why that I think you could do it would be on the page level. You could add a noindex nofollow to the page itself.

You can generate it automatically too and have it fired depending on the url by using a substring search on the url as well. That will get them all for sure.