I consider using IIS Dynamic IP Restrictions Module in order to make it hard for DoS (Denial of Service) attacks. But I am not sure how that would work out for search engine bots like Googlebot.
In the comments is was mentioned that this could be done by whitelisting google's user agent. This is a bad idea: lots of bots can impersonate it, and then will be able to dos your site.
Looking at the feature list of this script, it seems that it uses two criteria to determine whether it's a dos attack:
For google, you can easily limit both of those things to below the threshold that the script uses by setting a custom crawl rate in google webmaster tools. This will mean that google will not crawl your site as often, but they wont overload your sever.
I'm not sure what you could do about other search engines, besides making sure that the thresholds for your script are higher than the crawl speeds that they use.