Personally, I dislike afkers, a lot. Namely for some of the reasons already mentioned; them wasting a crew space, them not actually playing the game, etc.
I honestly do believe that being able to boot someone off your own ship is quite preferable. With restrictions to prevent abuse of course, like a 2/3 vote requirement or the ability to report abuse, or if all else fails, make some way that active participation is rewarded while active laziness is punished.
Also as a side note: my preferred method of removing parasites is with flagships, letting the afker(s) get sent to jail by the crew and then getting the loot from the ship after finishing the enemy crew!