In Google Sites, I can disable comments for a page by clicking Settings, Page Settings, and unchecking "Allow comments". How do I uncheck this option for all pages at once, i.e. disable comments globally on my site? Do I need to disable comments on a per-page basis?
There isn't a global setting for comments in Google Sites, so the comments should be disabled page by page.
You could disable the comments option page by page manually. Unfortunately looks that there isn't a method to do this automatically by using Google Apps Script.
To avoid this problem in the future, create a page template with the comments option disabled then use it to create the new pages.