This is a first. I am going to fall on my sword partially. I'd not considered fully the problem of the 9/11 conspiracy theory support that Jones appears to have provided via petition. And I agree with both comments from Scott and Clancy that this indeed is a problem.
I'd rather admit being wrong with a hasty post, than to attempt to offer support to someone who, as Clancy noted, "couldn't provide an adequate answer to very real questions...." That is an excellent point. Jones' remaining would have been a complete distraction to the Obama administration at this critical juncture in the health care madness.
I still think that we are moving toward a place where left wing activism is coming to be seen as unpatriotic and right wing activism patriotic, thus leaving those on the left open to greater scrutiny when they attempt to move into government service. That is a problem, because I think that both sides believe that what they do is for the benefit of the country they want to see come to fruition. And to suggest that the left is particularly problematic is completely out of bounds.
UPDATE: Here is an interesting take on Jones (and Glenn Beck) by Arianna Huffington.