Keep in mind this C130 was VERY old, and was on its last flight to AMARG in New Mexico for mothballing. In fact it was probably one of the least-automated C130s flying today so any sort of hacking of the FMS is less than likely. Most likely reasons IMHO: Broken control linkage, shifted CG, loss of hydraulics, rudder actuator failure, flaps set incorrectly.
Depends on what sort of INS sensors the autopilot on this particular C130 relied on and if the plane was flying with any sort of autopilot at the time. Theoretically, certain MEMs-based INS systems could be disrupted using electronic warfare, but doubtful this thing was using MEMs-based INS. C130s also have varying levels of EMP-hardening that would protect it from all but the most powerful of attacks.