If I discard Vet Captain to gain a command token, and the ship that started with him gets destroyed, my opponent still gets the points for Vet Captain, right? Even though it's been discarded.

I'm pretty sure it would be, but just want to make sure.

Yes.

This is just like in X-Wing.... if a ship is carrying bombs or missiles and has fired it, if you kill that ship, you get the full points cost including the points for the spent/discarded ordnance.

EDIT:

p.13 RRG " If a ship’s upgrade card is discarded, it is flipped facedown but remains equipped for the purposes of scoring."

Excellent, I was unaware of that ruling. Thank you.