I run Openfire 3.9.3 on Linux (CentOS 6). I also use Pidgin 2.10.9 and had this same issue this morning. I found a way to remove the ghost sessions manually, one at a time, with the affected user's Login and Pidgin.
Turns out that I appeared logged in with 2 other sessions and away for 12 days. When the "Sessions" list on the server didn't show these, I proceeded to troubleshoot. I then stumbled onto your post, and found that others were mentioning the Ghost Sessions being related to the auto generated Resource ID's.
I found that if I modified my account in Pidgin to login with the Ghost Resource ID (grabbed from someone else using pidgin) I was able to then Logout of that Ghost session.
I had 2 ghost sessions so I did the following:
1) I grabbed my Resource ID's from another user's Pidgin's roster list (Spark does not show this information to my knowledge)
2) In Pidgin went to "Accounts > Manage Accounts" and unchecked the "Enabled" checkbox next to my Openfire account
3) Clicked "Modify" on the Openfire account
4) Placed the Resource ID (8e7614f9) into the Resource field and saved
5) Reenable the account with the "Enable" checkbox
6) Unchecked the "Enable" checkbox next to my Openfire account
The ghost session was now gone. I had to do this again for another autogenerated resource ID, and then I was completely logged out without having to restart the Openfire server.
I then left the Resource ID as something manual, but it seems that there's another issue looming over this on a page that is linked to this issue.