Edit
I did a clean install of windows and found a much easier way to not mess things up. This is useful now that Windows 11 no longer gives you the option during installation of not using Onedrive.
First, go to onedrive settings -> backup -> manage backup, then click "stop backup" for all three folders (Documents, Desktop, and Pictures). Then, if you go to onedrive settings -> settings -> choose folders, you can easily uncheck those three folders (the only one you can't uncheck now is personal vault, but that's fine to ignore).
After this, if you go to explorer and right click any of the three folders, under location, it will no longer be under "onedrive".
Original answer
I had this exact problem, using Windows 11 in August 2022, nearly 8 years after this question was asked. After a good deal of struggle, I was able to solve this definitively.
For me, what happened was that I uninstalled Microsoft Onedrive, but because it was still syncing, it left duplicate Documents and Pictures folders in my explorer. There was an option to set the target back to the original non-Onedrive versions, but that option did not work, complaining about something like "target doesn't exist" or something.
So I tried reinstalling onedrive just so I can properly disable syncing. To add to confusion, there's an app in Microsoft Store that is ALSO called Onedrive, but that is actually completely unrelated, and is merely a UI to the ONLINE Onedrive, NOT the one the syncs with Windows. In order to reinstall the one that syncs with Windows, I needed to go to C:\Windows\SysWOW64\InstallOneDrive.exe or something like that. After re-installing that, disabled syncing for Documents, Desktop, Pictures, etc. Note that disabling is also highly nontrivial and requires some trickery, described in another answer. TLDR: in the "choose folders to sync" settings of the Onedrive sync app, you need to EXPAND Documents and uncheck the "Files in Documents" SUBcheckbox, since if you attempt to uncheck the top-level Documents checkbox it will complain that "this is an essential folder and you cannot stop syncing it" or something like that.
After doing the above, I uninstalled Onedrive again using the "add remove programs" settings. Actually the when I tried to uninstall, it complained that "C:\AppLocal...\InstallOneDrive.exe doesn't exist, so cannot uninstall", or something like that. However, I then went back to the similarly named exe file under C:\Windows\SysWOW64 and tried double-clicking it, and THAT complained that "you already have a newer OneDrive installed" or something. Then I closed the "add remove programs" settings, then re-opened, and now uninstalling worked. Not sure what happened there, but these are the steps in case others run into this same issue.
After all the above, I went back into Explorer, and my Documents, Pictures dirs were all successfully de-Onedrive-ified.