I see for the Equinox a card for Maxwell Burke as a Captain. However, to use his action his card is discarded. I know he only costs 1 SP, but still, wouldn't he be more realistic as a crew upgrade? If he gets removed do you automatically replace him with a Skill 1 Captain?

Yes you would. Some people might think the 1 fp pitch is good for them

Sideboard shenanigans!!

Actually, if your captain is discarded, you actually have a ship with no captain and it is considered to have a captain skill of 0.

His noble sacrifice (of other lifeforms) for the benefit of the ship and crew will be remembered!