Aversion to scent is a protective mechanism. maybe he is allergic/sensitive to coconut? or perhaps it triggers the memory of a bad experience; maybe a painful rash that was treated with a cream that smelled like coconut?
Maybe you should check to see if he does have an allergy.
But to be honest, he sounds like a normal kid. Kids always have varying preferences when it comes to food, but that doesn't mean they know what's good or bad for them. When I was young I used to hate the taste of broccoli and cauliflower, but I'm glad my mom forced me to eat it because its healthy!
You might try different brands. I have a smell aversion to some brands of coconut oil because they smell soapy to me. I get a jar home, open it, and can't eat. Other brands smell delicious. I've also had a problem with older coconut oil smelling terrible. Even within the same brand: sometimes it smells ok, other times it smells bad. My favorite so far has been Dr Bronner's coconut oil. Second favorite was Tropical Traditions. The Spectrum brand has been the spottiest for me, but perhaps it tends to be on the shelf longer at the store. Whole Foods's 365 brand has been mostly good to me but sometimes bad.
When I first began using coconut oil I found that the smell was near enough to make me want to shut the stove off and leave the room. After about a week of use, the smell no longer bothered me. I've noticed that different brands do have different pungencies, as Sara S. mentioned, so you might try switching things up. However, after not using the oil I found I liked best for a week or two (just fell into a routine of butter and lard), I bought a jar and again had the same smell aversion as when I first started using coconut oil. I have no idea what causes this, but, for me, after some exposure, I don't even notice it and even start loving the smell. Good luck!
I have a scent triggered allergy to coconut.. when i smell it i start to gag and my throat will swell shut.. if he is crying and gagging you may want to take him to an allergist to do a skin test to check.. i lived 25 years before this allergy hit me and its supper dangerous to leave be even for a few minutes without an epipen handy. in the event he has an anaphalactic allergy to it you would be prepared and not have to go through that trama