In my experience, low makeup guys will still develop fine during the first few years pro. I would watch out for guys with the combination of low health and low makeup though. Injuries stunt the growth of prospects almost as much as mismanagement. As long as you play him in the minors as many games as possible, he'll develop.
I would not consider taking a stud out of my top three just because of low makeup. There would have to be other warts.