He did it at the request of the network, NBC wanted minorities on the bridge! Both pilots featured exclusively white characters except for minor appearances (like George Takei who did appear in the second pilot as an unnamed science officer).And again, I don't think that the audience wanted to see a black woman either. But he did it anyways.
It was also Roddenberry who decided to ditch Number One, he could have kept the character, NBC liked the idea, they just didn't want Majel.
Don't give Roddenberry too much credit, he didn't care about diversity or women in major roles although he liked to pretend he did and take credit for it after the fact.