I have an aggregate site on a linux server that pulls in feeds from a universe of about 2,000 blogs. It's in Wordpress 3.4.2 and I have a cron job that is staggered to run five times an hour on another server to pull in the stories and then publish them to the front page of this site. This is so I didn't put too much pressure all on one server. However, the Google bots, which visit a few times every hour bring the server to its knees in the morning and evenings when there is an increase in traffic on the site. The bots have something like 30,000 links to follow at this point. How do I throttle the bots to simply grab the new stories off the front page and stop there?

EDIT- Details of my server configuration:

The way we have this set up is the server that handles all the publishing is an unmanaged instance via AWS. It mounts the NFS server and connects to the RDS to update content, etc. You get to this publishing instance via a plugin that detects the wp-admin link and then redirects you into there. The front end app server also mounts the NFS and requests data from the RDS. It is the only one that has the WP Super Cache on it.... The OS is Ubuntu on the App server and the NFS runs CentOs. The front end is Nginx and the publishing server is Apache.