I think everyone is going a bit overboard here with the analysis. While their could be some evil master-plan that is being laid out, I think the more simpler explanation is as follows:
Kelly plans on taking Mariotta, plain and simple. And if that is decided, than Kelly and the Eagles certainly know they are likely not winning this year or next. Like most QBs, MM will certainly need a couple years to get up to speed with the pro system before they can make a serious run.
Assuming that simple fact is what the Eagles brass believes, and they are game-planning for 2016 and beyond, then there is no reason to hold onto McCoy. Paying him $10M+ for each of the next two years will get you nothing. Why not ship him to a team for a young ILB that, in two years, could be the cornerstone of your defense for the next 8-10 years along with Kendricks?
Get rid of the players that won't be exceptional in another two years (McCoy, Herremans, Cole, etc.), and use the money saved to pursue young FAs that will be here for 4-5 years, and build a defense that will be ready to win when the QB is ready to win in a couple years.
Seems like a pretty simple plan.