I found an easier way to get the "without a scratch" achievement. What you must do is destroy the all the orange targets, but DO NOT go towards the ship with the yellow target after you finish. Instead, hang out by the two submarine holes by the start of the level. You can just catch the missles and fire them back at him, switching between the two holes. You will kill the sub and not have to worry about the research ship.
I understand this achievement isn't too hard to begin with, but this method might make it easier for some. Good luck on the 1K!
I realized I typed the title wrong after I hit post. If an Admin wants to fix it , that would be cool.