FV Thoughtful Comments adds front end comment moderation including sophisticated banning mechanisms. Say Goodbye to Disqus!
If you want to get the most correct display when deleting a comment and preserving it's replies, you need to use a theme which is using "cascade" display of the comments instead of "nested" display.
Thoughtful Comments assumes that each comment is contained in some HTML element with unique ID which is containing the comment ID, so it works with most of the themes.
Also, commenter name should not be in cite tag, so that the HTML highlight will appear properly and not as readable HTML (similar to code tag).