The missile has many many parameters to play with, for example, initial elevation and initial mode. Mode 2 is active (this mode is used as soon as the target's predicted position is inside missile's inboard seeker range. In active mode the missile will not avoid terrain at all (if this parameter was set to true). Consider also that cruise altitude is above sea level, not above ground level. The flight patron you may be looking for is something like that:
- Missile is fired upwards, 45 degrees elevation angle.
- Missile is initially fired in inertial mode 0 (it will climb to cruise altitude and then it will try to keep cruise altitude while flying to seeker activation point).
- Missile will try to avoid terrain elevations while flying in not active mode (2). This is not really needed if your flight patron is high enough over the terrain.
- Missile activates its seeker relatively close to the target, 600~800m inboard seeker range.
Anyway, as said, the mission you were looking for is already done and ready to download
here. Look for an attachment named laser_missile.intro.zip halfway in that page. That mission covers laser designation and missiles being fired behind elevations by hidden choppers. In this mission, the missiles need only an slight initial fire angle to avoid the mountains and island coast. So they fly all the time in active mode and do not even care to avoid terrain elevations.
In the same page there is another attachment named mando_missile_lab.Sara.zip (read the important NOTE in the post). You may use the tool preset there to set all the desired parameters for a missile and test them firing against several targets. Then you may copy/paste these parameters to use in your mission.