Yorke was trained to be a Navigator as a child by a secretive renegade house that had created the mutations that granted him his Warp Eye. Despite being a mutant he still embraced the Cult Mechanicus, and their Machine God Omnissiah. When he learned that they were going to attempt to mutate him further as an experiment of his genes he made a run for it. After the attempted theft of a shuttle he was press-ganged into military service by his house, even though he was still a child. He knew enough to navigate the warp and showed that he was quite intelligent after they inserted a cortex implant to sweeten the deal. All of this made him valuable enough to trade off to the Imperial military as a bargaining chip to solidify a contract. He would still be paid of course, but it was substantially less than normal.
With the exception of the unusual Warp Eye they failed to notice his mutations, but something about him was unsettling to them. At first nothing seemed wrong, and he did his job as a navigator with ease, shaving weeks off their travel times. As time wore on things only got worse as Yorke's movements became more and more fluidic and his mere presence spawned aggression in the crew assigned to work with him. After several months of service on board the ship no one wanted to be near him, even the captain, who decided that it would be better for the crew if he dropped him off at the nearest station to look for a new navigator. Everyone heartily agreed, and soon enough he was stranded at a station without a ship.
Some things i want just to note here:
Navigators NEED Those mutations( in the story it sounded like the third eye was merely beneficial for that), they are the only way to travel the warp. To explain it : The Navigators third eye is usually always closed. When they enter the warp however, he opens it and looks into the warp itself. The third eye turns the nature of the warp into something the Navigator can understand and navigate through( in contrary to the normal man who would go insane looking into the warp, as surely as someone going blind from looking all day into the sun).
Daring to encourage Mutation is deemed heretical and even if the Cult Mechanicus would do this, the end of the story would be a nice bonfire. Of course only if they did it overtly. Even if it was a more radical sect( in this case REALLY radical Organicists would come to my mind, maybe some Logicians far of the moral scale) of the Mechanicus they would do such things as secret as possible.
The Navigators Houses, being known mutants are controlled tightly. and with tightly i mean, so motherfucking closely monitored that they have a chemical analysis of your last visit to the toilet. No Imperial Navy Captain that would be of sound mind would employ a Navigator of unkown or doubtful inheritance. Especially not if it is a Renegade House that operates not completely legal and is acknowledged by the Administratum. Houses such as those would sell off their ware to the more unsavory characters or such people without the money to buy even from a small Navigator House.
Although it doesnt seem like it, The Navigator Houses most important good is its breeding stock. Nobody of the established Houses would sell off a half-trained Navigator( im not sure how long usch a training takes but a kid seems like too early). The possibility of losing that Navigator and more so the loss of Reputation ( for selling off unlucky or incompetent Navigators) would damage the house more than they would gain. Of course a Renegade House will mostly be too desperate to have such tight morals.
These are just some things i wanted to note to your story as a consideration...XP