Yes, if the Sox acquired Samardzija they would have to extend a qualifying offer at the end of the 2015 season in order to receive a draft pick, but that's a no-brainer. A healthy Samardzija is never taking a 1 year $16M (estimated) deal, and even if he did, that would still be fine as far as the Sox are concerned.
So ultimately, you are trading for one year of Samardzija plus a draft pick, and Beane is certainly going to take that into account in calculating his return.