Can't I kill the two default goons on my bridge? They throw off my bridge crew entirely. I don't like blue shirt blonde girl and gold shirt blue guy. Can't I send them on a mission and let them die, their names aren't in the opening credits!

To kill goons you must get the captain angry. He will then, in a fit of rage, disband the ships crew stealing assets in the process.

They are "replaced" as you fill your crew. If you are like most players you only need 4 crew members ever. So you probably didn't recruit any more. Grab a few of the free ones as you level and make their outfits match. That should do the trick. Also I found some of the bridges have less "stations" for NPC crew members.

No, I have a full crew. For my level at least. But there's always free stations and they are always there.