In this sentence, "come up the hard way" means worked his way up the ranks (promoted) by working hard. He did not get promotions easily.
Anytime you hear that a person has "come up the hard way" you know that person has earned all the privileges or positon because he has worked for it.
Joe hasdcome up the hard way in the company, so he deserved to be president. But the owner gave that position to his son, who doesn't know a thing about the company.