I do three things to make sure they are all the way removed. First I go to the Wp settings and turn commenting off, then go to comments.php and remove everything from that file except the first comment. Then I search and remove everywhere is calls for the comments;
This is the string I search for: ” <php comments_popup_link “
Then there is no way for comments to ever show and there is no way anyone can try to comment. I would only do it this way if you are for sure you never want comments on your wp site, even int he future.