I'm a sabermetrics guy, and I still believe in chemistry. Some things just can't be quantified with a stat.
People can't tell me those Bonds/Kent Giants teams wouldn't have performed better had they gotten along.
I would definitely use it, but obviously agree with others that it should be able to be turned off, of course.
Great points and I hope your stuff makes it in... I'll see if I can't come up with my own list of stuff to help out, too.