It's tricky, but most of these random insta kill things can be solved with the right crew member (Maybe even their experience helps, I forget).
When you start off think of your crew as being all red shirts living on borrowed time. Getting a good mix is important! You need an engi at the very least. It is a lot less fair than say, Spelunky, where you can see how almost everything works by looking at it but I had that feeling you have as well and it annoyed the hell out of me until the fourth or fifth run and I worked it out. Diversity!