YOu're right, this is indeed a challenge. But the benefit is often they're not getting screwed by bad planning, over promising, etc. Afterall, those are the kinds of decisions that really burn people out. Instead, they finally get a chance to have a say. Also, I'd argue all the information you're talking about that is potentially decreasing morale is already out there, it's just not being officially recognized/aggregated. At least this way, it's surfaced, and management understands what the perception is out there and can address it head on.
Bottom line, these aren't for everyone. One of the first questions I ask when someone expresses interest is what their culture is like and how humble their leadership is. If they're ready for it, prediction market can be transformative. But if they're not, they can fail - and we've surely had plenty of those projects too!