Poindexter is a problem. He has a history of devoting resources to covert operations against the will of Congress. I am not comfortable having him in that position because I believe he will abuse his position.
The research that Poindexter is funding is a problem. It is research that is intended for specific uses, and with Poindexter there, those uses are likely to be things that I do not want to see.
Claiming that the use of the research is used is in the hands of Congress and the President is also wrong. Given Poindexter's convictions, we can assume that Congress won't necessarily have much of a say.
Taking your comments from the top:
1. Re: Poindexter in charge:
So [link|http://www.darpa.mil/iao/TIASystems.htm|TIA] wouldn't be a problem if, say, Larry Lessig was in charge? I don't think you really believe that.
2. DARPA is very different from the White House. DARPA funds research. That's all they do. They have no say on policy. The National Security Adviser, Poindexter's previous job, has a policy mandate. Poindexter at DARPA has absolutely no say on what the DOD or any other organization deploys.
3. Congress controls DARPA's budget. [link|http://www.darpa.mil/body/pdf/FY03BudEst.pdf|2003 DARPA Request (373 page PDF)]. "These technologies will be tested and integrated into the Total Information Awareness (TIA) System funded in PE 0603760E, Project CCC-01." CCC-01 is described starting on page 267 of the PDF. Its budget is $76.6 M in FY 2003 (which started in October). Congress can take this money away, or the President can modify the request.
Don't let the fact that you don't like Poindexter's past get in the way of the fact that the best way to fight TIA is by letting Congress and the President know. In other words, don't shoot the messenger.
My $0.02.
Cheers,
Scott.