I was watching a show a while ago and they had created a program to determine which employees to keep and which to get rid of. There was one guy who scored really low and he was the clear choice, but it didn't take into account he made the others around him better. As you said, things like that can make a huge difference over the obvious stuff.
I worked for a small company that had a group of office staff, and they essentially forced one out and treated them badly. The person was the social glue that held the rest together and once gone, the demise of the company was inevitable.
Yikes, that's too bad!