Actually, to skip the skipper missile navpoint, you have to request permission to land at the point before that, and manually fly into the hangar at under 100 (IIRC on the value). Hitting autopilot to land will just take you to the next waypoint, which is what you were trying to avoid. However, by doing so the mission is considered failed, and you go to Delius to play in the rocks.
The alternative way of doing that mission is to manually fly ahead to the waypoint with the 'vette, instead of hitting autopilot to get there. By flying manually, you get to leave the Victory far enough away that you can engage the corvette at your leisure, before the missile launch is triggered.