Complicating the "Microsoft corrupted the virtuous Skype" story is the fact that Skype appears in the PRISM slides dating to before Microsoft's purchase of it.
Skype appeared in the PRISM program on 2/6/11. Microsoft bought Skype on 10 May 2011. Very fishy dates? You bet.
If that isn't the source of confusion, I don't understand your point.
In reality you would do a lot of work with the company you're attempting to buy. If for example Skype promised they could change the network to enable wiretapping yet they are unable to, then MSFT could cancel the deal. Or indeed for any of the reasons outlined in the original press release about 'forward-looking statements'.