Those entries at the top of the sidebar are your Safari Tab Groups; Golden Gate's sidebar shows them above the Bookmarks section. The reassuring part first: they only look like they contain your bookmarks. A tab group holds live open tabs, and deleting a group does not delete a single bookmark; your sorted bookmark folders below are untouched.
To remove one: right click (or Control-click) the group's name in the sidebar and choose Delete Tab Group. Its tabs close with it, and since the pages were never bookmarks-by-association, nothing in your Bookmarks changes. Repeat for each group you do not want.
Two limits to know about. The first, default group at the top cannot be deleted; there is always one unnamed group that your regular windows live in. And if you only want them out of sight rather than gone, there is no sidebar setting to hide the section; collapsing it is as far as it goes, deleting the groups you no longer use is the real cleanup.