I realize this is a really old thread, but I found this when I was searching the same thing and want to help anyone else who may have this issue in the future.
I have found that if you cannot delete an attribute from an attribute set, simply follow these steps.
1. Create a new Group inside the attribute set.
2. Name it whatever you’d like. (I name it trash)
3. Move any attribute into the group.
4. Select the group and click the “Delete Selected Group” button.
NOTE: This does not work for system attributes.