The "rules" bit:
1. If you don't have time to read or address reader comments, consider that you might not have time to blog.
2. If you have a strict disclaimer or instructions for commenters (what behavior or content won't be tolerated), but don't have time to enforce these policies, then really don't bother blogging.
Theologica and Boundless Line are two prime examples of what happens when you don't consistently respond to out-of-line or heretical comments, and in the case of Boundless, what happens when you don't enforce your comments guidelines. The moderators end up suborning heresy, the comments sections spiral out of control, and the constructive discussion gets choked out by confusing, contradictory comments by believers, unbelievers, and pseudo-believers.
So, do you 1. address and refute out-of-line or heretical comments, 2. delete them, or 3. let them slide?
#3 is irresponsible and foolish, and either 1 or 2 works. I lean towards deleting (although a blog that's turned into a public forum would want to be crystal clear about the standards for deletion). Heretics who find themselves being blocked will keep moving until they find somewhere else to comment.
And really, have you ever heard a new believer say, "You know, I was an atheist until I started commenting on this blog..."?