I think you already know this, but Discourse updates the DOM as you scroll (a bit like UITableView) by adding/removing items. The browser's search bar would only find stuff that's currently in the DOM.
I think it only does it on threads that have enough posts that they're not all loaded at once. (in which case the browser's built in search won't be able to search the whole thread)
If you really want Safari's search in that case (e.g., you intentionally only want to search the part of the thread that is loaded) then pressing Command-F twice switches to Safari's search field.
I think the current behavior is useful as most people probably wouldn't realize that Safari's search isn't necessarily going to find every occurrence of the search string within a thread when there are a lot of posts in a thread.
I appreciate the point about not all the posts being loaded in, but the built-in Discourse search is a poor replacement for a browser search. It doesn't even default to searching only the current topic, for example.
If that's still an unacceptable behavior, I think an extension like StopTheMadness could help, which allows disabling any hotkey hijacking, and even on per-domain basis, if I remember correctly.