Vader was worried that Fett would injure his other (more valuable) captives.
According to the film's official [junior novelisation][1]junior novelisation, Vader's concern was that in his eagerness to shoot Chewbacca, Fett could hit either Leia or Han, both of whom have intrinsic value.
Realizing what was about to happen, Chewbacca let out a wild howl. He threw his right arm out to his side, striking a stormtrooper with enough force to launch the figure from the elevated platform. Before anyone thought to react, Chewbacca lashed out with his left arm and disposed of a second stormtrooper in the same fashion.
Across the platform, Boba Fett brought up his blaster rifle, but Vader — hoping to preserve his other captives — lashed out and grabbed the rifle’s barrel, forcing the bounty hunter to aim away from the melee.
[Star Wars: The Empire Strikes Back - Junior Novelization)][2]Star Wars: The Empire Strikes Back - Junior Novelization)
[1]: http://starwars.wikia.com/wiki/Star_Wars_Episode_V:The_Empire_Strikes_BackInterestingly, this is (junior_novelization [2]:somewhat) contradicted in an earlier Q&A with Pablo Hidalgo in http://starwars.wikia.com/wiki/Star_Wars_Episode_V:_The_Empire_Strikes_Back_(junior_novelization)Star Wars Insider #75, where he says that Vader's main motivation was simply to remind Fett that he'd already told him not to shoot without orders.
Q. In The Empire Strikes Back, why does Vader stop Boba Fett from shooting Chewbacca in the carbon-freezing chamber? Was it the fact that C-3P0, Vader's droid, was attached to Chewie’s back?
Although a stirring short story that appeared in Star Wars Tales #6 suggests that Vader did indeed recognise C-3PO on Cloud City, there really was no connection between the Dark Lord and the golden droid back when Empire was made. Vader's restriction of Fett was primarily meant to show just who was in charge and that no-one fires a shot without Vader's say-so. Granted, it's hard to read expressions through immovable plasteel armor, but it looks more as if Vader is reminding Fett about his “no disintegrations” order than as if he’s having gooey memories about a protocol droid he once built.