I'm not familiar with the inner workings of planes, but from what I've gathered, the timing of disabling the two tracking systems, which are on either end of the plane, is just about the same time it takes to get from one end of the plane to the other, and disable the 2nd tracking system (blackbox).
Therefore, it would be a great coincidence that both of these tracking systems would be disabled at the same time. It seems therefore that the most logical explanation is foul play.
I thought/hoped the same as you, that some sort of failure resulted in the tracking systems failing as well, and then the plane crashed, but it sadly doesn't seem as likely given the timing of events.