Hello Krileon,
I would gladly give you super admin status to check out the bug, but I'm in the middle of developing the site and it would cost too much time to have somebody figure out the bug.
However, we had an issue within the database table for groupjive that caused a few problems. We eliminated the field and all problems were gone, it could be that the group deletion was caused by this faulty field as well. As soon as I have time to check out the issue, I'll do and than I'll keep you posted.
Thank you.