That is an incredible draft pick, if you'd sold him he would have been worth $2-3m easy (maybe more). One of the best you can get, very nice!
A player like that ideally needed level 6+ trainers because he had the potential to be one of the best players in BB. So it's a shame he won't reach his absolute maximum potential. But you were right in what you did, it's your player and you should play the game the way that gives you the most enjoyment.
You're doing a good job training him, he's still going to be a great player, probably a NT player. I don't think his salary is ever going to be a problem - he'll have a very affordable salary for at least 3-4 more seasons, possibly longer, and by then he should be good enough to help you promote. Even if you never get out of III, you would have the option of being a "farm" and putting all your salary into that one player.
It sounds like you're making good progress now, continue what you are doing!