Ha! See, you can just choose to never play those stupid tower defense things if you don't like them. I played the one from the story mission and one more later on. I decided that I didn't like it so I just made sure to keep my notoriety down so it would never trigger the takeovers. Now that I've got a master assassin in each den, I don't have to worry about it AND it automatically checked off the challenge for doing 3 den defenses once I did so. It's almost like they knew that nobody would like those or something.
So, long story short, avoid triggering the defenses, and you'll still be able to "complete" the challenge for winning 3 of them without actually doing so once you've trained up your assassin buddies.
Sweet. Thanks man. I was SO goddamn slow at setting up my guys and blockades, that I could never get past the final "tank" wave. It took me a couple tries to get past the tutorial segment, and then accidently got my notoriety too high and had a helluva time defeating them for real. Those segments is what made me set it aside for a later date.
Thanks again for the advice.