One of the comments in the Fed Baseball article mentions it is interesting that Beane and Rizzo deal. Those sort of deals make sense for both teams' managements. They value players differently, so something Beane wants is of lower value to Rizzo, while something Rizzo wants may not be as highly valued in Beane's mind. I'm not so up on the economics lingo as I was in college, but I think there's theory about optimality and utility that applies here. I'm hoping mathguy or someone bails my butt out here.
The Gio deal might be a case in point. I don't get the impression that either Milone or Norris were highly valued by Rizzo. Milone's just a junkballer, and Norris had the Ks, low average, and his walks were not valued so much (compare him to Rizzo boys like Desmond, Morse, Lombo, and Espinosa). Gio has great stuff, but Beane may have seen him as getting expensive, put too many guys on via walks, and a sell high guy who was having success due to the ballpark he pitched in. he may have said he prefers a guy who does not chain walks together in the coliseum, safeco, and the A because anyone can suppress HRs there. Couple that with maybe with a belief that Norris was disciplined enough to get more out of his skills, and there was a basis for these parts of the deal centered around Cole and maybe Pea****.