I can't speak to Roddenberry's actual motivation for giving Pike that particular line, but I like to think that it was put there to make Pike relatable to a 1964/65 audience - "See, we're X years in *THE FUTURE* and we have a woman executive officer and a guy with pointy ears, but don't worry, guys, our lead's still just like you folks at home."Re: Yeoman Colt: "She does a good job, all right. It's just that I can't get used to having a woman on the bridge. No offense, Lieutenant (Number One). You're different, of course."
Star Trek was not always full speed ahead on equality. But they tried.
I also note that when "The Cage" footage was reedited into "The Menagerie" two-parter in 1966, that whole exchange was eliminated from the aired version. No one except studio executives and convention and college lecture audiences to whom Roddenberry had shown his black and white 16 mm print had seen that segment until the mid to late 1980's. Given those circumstances, should we really give that line of dialogue so much weight when it comes to characterizing Pike?