Yes, I agree. People have to beware when watching a show (or movie) from decades ago that they are watching a show that is a product of its time. Things that would be completely unacceptable today simply weren't back then.
We have two choices. One is the more extreme....don't watch anything made before 2000, or 2010, or 2019, because as society changes what is acceptable changes. I think of the whole "Snow White" debate from about a year ago when some actress, Kristen Bell maybe, won't let her child watch Snow White because the Prince kissed her without her permission (sort of a bizarre complaint as the alternative was to let her die and she obviously wasn't in a position to grant position....but I digress). But that's one way to approach it.
The other is to watch them and just be aware of when they were made and things that were acceptable back then would not be today. In the 1960's it wasn't all that common for women to be in significant positions on military vessels. Pike's comment in 1964 when it was made, was likely not controversial at all. In some ways it goes back to something featured on one of the Tom and Jerry Spotlight Collections, I think Volume 2--they have Whoopi Goldberg make a statement about how those old cartoons portrayed Mammy Two Shoes---that basically it was a product of its time and to pretend it didn't exist would be to pretend racism never existed, which would be just as wrong. It's ok to enjoy old shows as long as you keep it in perspective. Liking "The Cage" does not make you a chauvinist. You can disagree with Pike's comment and still enjoy the rest of the show.
Probably the best thing for current writers of Star Trek to do when dealing with Pike is to simply ignore the line. It's obviously anachronistic today and while some have made a gallant attempt to explain it away, you can't really. It's probably just best left in the past.