If true acceleration is not noise in the system, what is it then?
The accelerometer sensor reading is part of the measurement of the state of your system, just
as the gyroscope sensor reading is.
So it should be part of the measurement vector, not the input vector
If you have a system model like this
x(k) = F.x(k-1) + B.u(k) + noise
z(k)= C.x(k) + noise
then any quantities you are actually able to measure to enable identification of the best estimate
of the state of your system, x, go into the z vector not the u vector.