So...inventory of possible causes....
Bomb
Manpad
Wing Spar Failure
Fuel Tank Explosion
Loss of Control
Mid-Air Collision
Meteor Shower
Turbulence
What did I miss?
Well, you missed pilot/crew error...
...which is always a possibility, and judging from the debris distribution and the manner in which the parts impacted the ground (falling near vertically with almost no horizontal component) it would seem that you couldn't at this point rule out a high-altitude stall followed by overstress of the airframe during recovery attempts.
A view from the inside (flying KC-135s for 15 years).
The mishap aircraft was a bit over 100 miles downrange from Manas which means they would have reached and leveled off at cruise altitude. In a refueling mission this is often an action point. Upon leveling off we would check and confirm mission timing (to meet either original or revised timing for a standard point parallel or enroute type rendezvous or to support a simple arrival time for an anchor area "on station" period). And we would begin making decisions regarding where to move fuel quantities (if necessary) in anticipation of later refueling activity (i.e. draining fuel from the wing tanks to the aft body tank which both prepares it for offload and moves the aircraft's CG aft for more efficient cruise flight, and possibly draining some of the center wing fuel into the forward body tank which is sometimes done to counterbalance fuel drained into the aft body tank).
Here's how I could imagine pilot error entering the picture in this incident: Upon reaching cruise altitude the crew may have discovered they were running early for the rendezvous (either original or newly revised timing). So they might have pulled the throttles back to slow to endurance mach speed. If a distraction occurred in the cockpit at this point and the aircraft continued to slow a high-altitude stall could have taken place. If after leveling off they'd also begun draining fuel aft from wings to the aft body tank the situation could have developed rapidly.