What is wrong with players looting cyberware from corpses? As long as they know an organ legger or some ghouls, it shouldn't be a problem.
There are two problems that come to mind - one story-based, and one game-based. From a story standpoint, getting a reputation of killing people and selling their parts is likely to have
you chopped up for parts the first time you're on the losing end of a fight...and give you quite a bit of notoriety even if you avoid that. From a game standpoint...SR module writers seem to love stuffing bad guys with Delta-grade cyberware. Even though you sell it at the Used rate, 5 points of Delta-grade cyberware (the equivalent of 10 points of normal 'ware) is going to add up to major Nuyen. It's the equivalent of letting the characters grab a high-end deck and fence it.
While my Missions character hasn't looted cyberware from a corpse, there was one piece of 'ware that was already removed and conveniently left on a table. I consider that fair game. My fixer gave the team 30% of the price for the Used 'ware (another piece of former Delta cyberware). It was a relatively small amount of Nuyen (especially splitting the profits among the entire group), but any unexpected bonus to profits is welcome.