I have tried Chrome and have found Safari more usable. Yes, these sites are bookmarked to be read later, but the "X" that can remove a bookmark has disappeared.
I find Safari to be too slow, and thus don't use it much at all. But, not sure what you mean by "these sites are bookmarked to be read later". I always thought a bookmark is always there, in one's list. But, if you mean it is in Safari's History file, well, that is something different.
OK, I just ran Safari. I am using the version that comes with Sierra.
In any event, on the heading line, after arriving at a site, the X turns to a "kind of circle" symbol, which would be used if I want to reload the page. To actually delete the site, I chose "Edit" from the Bookmarks menu (click on Bookmarks), and after getting a list, I just highlighted any one, and then select "Delete" from the Edit menu. It then gets deleted.