Quarantined root directory on primary drive? I've been experiencing performance issues on my mid-2011 mac mini (running El Cap) for a while now -- beachballs, spotlight issues, general slowness -- and have been so far unable to discern the actual cause (this is, in part, why I haven't yet upgraded to Sierra). I just noticed that the root of my primary drive is marked as quarantined:

andy@Aurora[14:57:14]: $ ls -ldeO@ /
drwxr-xr-x@ 40 root  wheel  - 1428 Jan  7 16:20 /
    com.apple.quarantine      68


Is it possible that this is the cause of my problems? And how would I go about fixing it?
Before doing anything else I would strongly recommend you backing up all your files and (after that) double checking for malware on your Mac.

You can remove the com.apple.quarantine attribute with xattr -dr com.apple.quarantine /.
For a more in-depth explaination of the com.apple.quarantine extended attribute, see this answer.