The site is maintained by very few people and they are away most of the time. So if for some reason the auto-refresh 'broke' then the site would be down or hard to use for a long time before it got fixed. In this form it's much less likely to have that happen.
Our thread system would make it hard to manage for some readers and I have no idea how it would affect those who use phones on the site. It could also lead to this site becoming more of a chat-place which is not what CYS is and I personally see no point in having an auto-refresh if you can literally just push Ctrl-R, F5, or right click the tab and refresh that way.
It's really not that hard. Here's a few reasons why I will not support auto-refreshers with no particular rank of importance.
1. It takes away control from the user and does this action without permission.
2. Depending on the refresh, it can force a user back to the top of a page.
3. It uses up needless bandwidth.
4. It causes people to lose their 'spot' on the page/thread.
5. CYS is far to small to be bothered with such a waste.