Yep, you want the whole thing to act like a system not a bunch of parts. Energy savings and a comfortable environment really depends on this. A poorly setup system can be a nightmare for the maintenance staff.
Not saying it's not a good idea, just saying that in reality I've seen these systems work very poorly together in most office environments I've been in.
If I ever teach a CompSci again, I would think about making a climate controller a problem set. My first choice is a storage building controller, but this would be interesting.