Edit: The Tor Project didn't see the CMU/SEI attack while it was happening. Maybe it was too subtle. Maybe the network is too chaotic. But I have no basis for saying that they ignored it. Still, maybe the Tor network needs an IDS.
Sounds like they did know?
Not that they knew what they were doing - they seemed to have suspected something, but made the decision that it was a small enough fraction of the network to not worry about, but obviously in hindsight they were wrong about that.
In retrospect, more monitoring seems an obvious approach. But that would probably hurt performance. And threaten security and anonymity. Maybe there's a middle ground.