[0]: http://www.certificate-transparency.org/certificate-transpar... , Certificate Inclusion Check
[1]: https://groups.google.com/a/chromium.org/forum/#!msg/ct-poli...
But this thread is operating under the thought experiment that the NSA already owns LetsEncrypt. And in reality-- at least according to the Snowden leaks-- NSA currently has classical MiTM capabilities. (Can't remember which program it was that was using some node between the user and the desired server to send back a forged response that would almost always beat the server to the punch.)
So in this thought experiment there are only two pieces of Triforce and NSA has them both.
These were called QUANTUM (with various sub-projects related to specific applications of that capability).
Also there _is_ a third piece of the triforce; certificate transparency logs; and those would be very difficult to compromise without the certificate transparency monitors noticing.
Totally agree with your point about trust being a very hard problem to solve, that's why CAs first came in to place, and now we have CT (which is not widely adopted yet). It is a problem that has no clear and definite solution yet.
Edit: Also, CT is no magical solution. It's just another "node" in the graph of trust we're establishing. As many other things have in the past, the CT system itself could also fail.