The control structure for a typical missile looks something like this:
As you can see, the PN-Guidance command is carried out by a dedicated acceleration controller. This has a couple of resons:
- First an foremost, the missile has some pretty complicated flight dynamics. The varying airspeed and altitude of the missile means highly varying dynamic pressure acting on the missile. At high airspeeds, minimal fin deflections already mean very high accelerations, while at low airspeeds, the same fin deflections almost do nothing.
- Most missiles are non-minimum phase systems due to the location of the fins at the rear of the missile. This means, when a fin is deflected, the acceleration will first be negative before becoming positive. This is a vicious effect, which the Autopilot is specifically designed to take care of.
The job of the acceleration controller is therefore to make the missile behave nicely. It can be designed such that the PN-Guidance always sees a relatively uniform missile behavior across all flight speeds, and altitudes.
Edit: After reading a couple of your comments, I would recommend the following: You can use what I wrote above to your advantage. Instead of explicitly simulating the acceleration controller in combination with the missile dynamics, you simply assume that the acceleration controller does its job right under all circumstances, and model the combination of these two systems as a low-pass of second order with a rise time of a few hundred mili-seconds. Additionally, you simply neglect the rotational dynamics (again, your assumption is that the controller does its job right). This leaves you with a modeled point mass, which follows lateral acceleration commands with the dynamics of a second order system. For some kind of realism, I would also include drag (perhaps the drag could be dependent on the g-forces the missile pulls). The resulting velocity and position can then be simply integrated from these accelerations. The resulting dynamic system would then be something along the lines of:
$$
\ddot{\vec{x}} = R_{IB} \cdot \begin{pmatrix} -a_D \\ a_y(t) \\ a_z(t) \end{pmatrix}
$$
with $R_{IB}$ being the rotation matrix rotating the accelerations from the body coordinates to inertial coordinates, $a_D$ modeling drag acceleration, $a_y(t)$ and $a_z(t)$ being the (commanded) acceleration of the PN-Guidance after it passed the second order dynamics.
Perhaps I can draw a sketch of the situation tomorrow if you are interested.