Try telling the ship to move directly onto the warp point, and then warp through it. Personally, I have never had problems getting ships to fly through damaging warp points. My captains are heedless of danger.
Actually, that's probably because I never have damaging warp points in long paths. The only time I move ships through them is when I am scouting an area, so the ship is given orders to warp through the warp point, instead of moving to a location on the other side of it.