Minato said he knew Naruto would control Kyubi because he is son, implying his son should have the same capacity as him to perform such a feat, something he showed to quickly display and master during his revival proving his words to be true. In my opinion the reason his body was going numb when he sealed half Kyubi is because he was already low on physical+spiritual energy, not enough to contain such a gigant entity of chakra properly. Doesn't mean however that he couldn't have used the mode, something he once again implied while encouraging his son during Pain's attack and proved during his revival