Sounds like your baby has a sensitive gag reflex. My nephew had the same problem with pacifiers when he was a baby.
He would gag when his mom put a pacifier in his mouth. His doctor said that he was sensitive to things put in his mouth and that since he was gagging with the pacifier he should not use one.
So since your baby is gagging when using a pacifier you should stop using it with him otherwise he could choke and that could be deadly.
Babies don't have to use pacifiers so if he can't use a pacifier without gagging then it's okay to not use it.
Plus you won't have to fight him when it comes time to wean your baby off the pacifier.