Hey there,

1) How to turn off comment system

You can do it by disabling 'Enable Comments for Questions' and 'Enable Comments for Replies' at Backend > EasyDiscusss > Settings > General > Comments. (Kindly refer the 1st screenshot)

2) Why is there a comment system if there is all ready a reply system?

The comment system is to let users give feedback and focus on the topic of the question/reply only. (Kindly refer the 2nd and 3rd screenshot for an example)

By the way, it would be the best you can include your site's access and FTP's access once at http://stackideas.com/dashboard/site so we can have a further checking if needed.