I would have guessed the settlement was to make things go away with some kind of closure. I would think that the symbology of the website shutting down would be sufficient to satisfy Apple. The lawyers for TS would still want to get paid (I don't believe all of it was pro bono). I suspect Apple would be fine with picking up the tab. TS's legal fees is probably less than 1 commercial run at the SuperBowl. Maybe we can blame TS if we don't see an Apple commercial this year!
From TS's standpoint, they are happy to get out the legal fees and like someone said before, TS was dead for some time now. The "journalists" will likely pop up again as some other rumor website, hopefully a little wiser.
TS will have got a good deal more than their legal fees paid. They wouldn't have lost the legal battle, they were breaking no laws, so they would have ultimately been covered anyway. This was a cash/stock deal to close ThinkSecret. Apple nor TS are going to say that though but it's the only plausible explanation. If the deal was something different it no doubt could have been told to the public.