Aside from all the server issues this morning, which is usually a harbinger of some incoming algorithm update, reddit also appears to have reset some user preferences.
When they first rolled out the user status feature, I went into my prefs and unchecked the box that says "allow other users to see your online status." When I logged on this morning, the green dot was back, so I went into my preferences and sure enough, the box was checked off again, as was the box that says "allow reddit to log your outgoing clicks", which I had also made sure was unchecked.
Noticed this as well but the servers decided to shit themselves as you mentioned so sorting it wasn't easy.
I know I already turned off the online indicator and while I can't be sure it was disabled while the servers were borked it was then disabled again once things were running properly again.
I'm left wondering whether the instability was the reason it re-enabled in the first place if perhaps an outdated redundancy with different preferences tried to take over when the main servers failed.