Space is dangerous. Plain and simple. It's up to the player how he deals with it.
To be honest I didn't come across that many triggerhappy pirates and I've been hauling, mining, smuggling for hundreds of hours. In most cases you pay up and all is fine; in some you RP your way out without any losses - just start thinking like your character would.
Then again, I've pirated the hell out of players and sadly, way too many (even seasoned players) don't give a damn about RP - they even ask you to shoot them. What can you do...
It comes in handy to have a few generic responses/ideas about such an encounter written down or memorized - then just act on the situation and you'll be fine. Dying too is part of the game experience, no shame in that.