Are you trying to implement PID loop for motor speed control. These delays have effect and also the motor/circuit lag will introduce more delay in the system. A proper tuned PID can overcome this.
In my experience with PID control, the derivative term is usually unnecessary or diminished. In discrete math it is mostly a noise maker, for that it is not worth improving it with 4-point approximation. Furthermore, increasing sampling rate worsens derivative term accuracy to practically a noise level. I think that 10kHz sampling rate should suffice for a motor control, while 100kHz is not enough for DC-DC converter application.