I experimented with this some more this afternoon and see a good workaround without compromising safety.
Edit WPILIB MotorSafety.java line 15 to be
Code:
public static final double DEFAULT_SAFETY_EXPIRATION = 0.5;
And then rebuild the WPILIB project.
The slight increase in time won't compromise the built in safety. This timeout can cause motor output to pulse, which will increase the motor temperature and you won't be running at top speeds.