It's not something you just want to throw in casually.
Why? The game isn't about teaching morality or educating the youth. It's about space dystopia. Throwing it in casually totally fits with the rest of the game.
It's about mass murder, and cute ship graphics can't hide it. Starsector encourages the player to be totally immoral and minimizes any political differences between factions. It urges players to plunder and destroy for rich rewards. Unlike many other games of this style (escape velocity, etc) there is no story, plots, or quests in which you can fight for discrete political goals or ideals. The average starsector player acts like a 7 year old playing GTA crowbarring pedestrians for hours on end. Combat is even encouraged as a primary playstyle, with peaceful activities only intended as side gigs.
Like when you sell 2000 tonnes of illegal drugs and destabilize a planet to cause a famine. (A lot of them probably resort to prostitution just to get a bite to eat, you know.)
Given the context of starsector, it is entirely adequate make slaves illegal for some factions as a way of highlighting the immorality. Include a running tally of crew and slave losses/kills etc as a witness to the players misdeeds.
But as you say, maybe the way of handling it that most fits the true spirit of starsector is this:
Just show crew in the salvage screen with no explanation.
Let the more optimistic imagine them as grateful volunteers.
Let the more pessimistic imagine them as something else.
There should still be a skill about increasing the number of crew you "rescue" during salvage though.