Is there anyway to disable the "inertial motion sensors" for a program, so that my program does not track the devices acceleration? I've noticed that if a user suddenly moves and then suddenly stops with the device the motion tracking becomes inaccurate.
Even if you could, "disabling the sensors" is not a good idea. And when you say "disabling" I assume you mean setting them to an initialization state rather than just ignoring the data stream. The 3-axis accelerometer and gyroscope data are fused with position data to provide your relative location during motion tracking. You have no way of knowing which of these data streams is the source of the inaccuracy, and just turning off acceleration would likely require a re-calibration of all sensors so that tracking (data fusion) is accurate.
Replicate the error with as much data as possible (speed, stopping time, orientation of the tablet, distance to the nearest object, nearest object characteristics, etc.) and report it to the project Tango team.