Bottom line: 

If the bottom line is to have a popular, successful internet news site - Does not a stimulating comment section add to viewership and number of times the site is visited? I do believe these are the trademarks of a successful site that translates into revenue.
Since, as you say, participants of the comment section are a tiny fraction of Civil Beat's viewership - then throwing it into the trash heap of history would not effect the "bottom line". I for one, have enjoyed this ever so brief experiment in viewer participation in public narration on the content of what is commonly known as the "news". 
Thanks for the experience!