>> I believe both of them(Nick Mathewson and Roger Dingledine) have very high ethical standards and are great people;
This all issue of cryptography is ethically complex. One the one hand, too much state power can lead to bad things, definetly. On the other, strong crypto/anonymity can be a risky tool at the hands of terrorists. And in reality , terror can cause very bad stuff[1].
Say you are roger dingledine, and a very convincing NSA guy comes to you, and shows you the evidence that some terror act , that killed X people, has used anon-remailers. How would that make you feel ?
Except the guilt, one implication would be that USG would fight hard against mixminion.
And then he offers you to lead tor, with funding, and explains that this is a network that is hard to break ,so even if NSA can break it, it wouldn't do it for silly stuff , only for emergencies.
You don't need to be a bad person to accept. It's seems like a perfectly ethical thing to do.
Regarding bottom-up or top-down:
My guess is that NSA has a top-down strategy regarding cypherpunks.That's the way military forces work. And it would make sense for this tactic to be part of their strategy.
[1]WWI , The iraq war, and the cease of the israeli peace process were all at least partially caused by terrorists. And we still haven't seen WMD based terror.