I took a read through, and will likely adapt it to my game. In other words, I liked it. The rest of this post is generally a quibble, although obviously by the length, a quibble that I think is important.
I do think that the ending could be problematic for a lot of players and/or characters. Some will do wetwork without much concern other than how it may hurt their karma/reputation. But others will have a lot more of an issue with it, and being put in a position where they agreed to an extraction and then are forced to either off the guy that they both extracted and helped arrange the extraction of, or else to have their reputation smeered ... well I know I'd be furious as a player. Changing part of my focus onto taking down Hudson would not be beyond the range of possible reactions -- depending on the character I was playing, I could imagine deciding that my goal with the character would be to capture, psychologically torture, then execute him, then retire the character as having turned too evil to enjoy playing him. Not saying that I'd go that far for sure, but it would certainly be in the range of reactions I'd consider.
Not saying that a GM should never do things like this in SR. The world is nasty, the corps just don't value human life for its own sake very highly, etc. In fact it is exactly that sort of moral question that can really elevate a campaign, forcing characters to decide where they stand on some of these issues. But this sort of thing should, IMO, only be done with careful forethought and the expectation that it could impact the tone of the campaign.
So .... I'm looking to use this, but I'm trying to decide how flexible I'll be about 'clever' player plans to keep the guy alive, and exactly when this would work well.