There are a few different ways the Diagram could be something other than what it appears.
One, it could be well-intentioned but wrong. Taravangian asked for the capacity to save humanity from the Desolation, but thanks to his fluctuating mental state he clearly doesn't have that capacity every day. He is assuming that he had it on Diagram Day, but there's no signed-and-sealed affadavit from Nightwatcher saying so. He might have needed some measure of compassion to find a solution.
Two, it could be leading humanity to a fate worse than death - more than one person has theorized that he's planning to lead Roshar to pure survival, by conquering the world and then surrendering it to Odium without a fight.
Three, it could be a trap. The entire curse of varying intelligence and empathy is a red herring, and what actually happened is that something else was working through him on Diagram Day, which may or may not have humanity's interests at heart.