The difference is that Star Trek has always had some kind of agenda at its heart: feminist, liberal, egalitarian, whatever. If you sell your programme or film as a 'progressive vision of the future', then don't use women as sexual objects to ogle at.
Star Trek Into Darkness and Star Trek 2009 are not overtly sexist, but they certainly contain problematic gender dynamics. I don't think modern-Trek should treat one half of the population as window dressing or (God knows the old versions certainly did). It's boring, it's anachronistic, and it's letting down young boys and girls.
Not really. What would really be "letting down young boys and girls" are parents who allow entertainment to substitute for the hard work of teaching values to their children. If any parent feels strongly enough about a particular value, they will take time to pass that value on to their children and ensure they've understood it. If that is done, then the children should not be so easily swayed away from that value by a 2 hour bit of entertainment. Indeed, if the lesson is well-learned, the children will raise the value conflict on their own (if they're too young, the parents are free to point out the conflict). However, the filmmakers have NO OBLIGATION to produce something that won't "let down" any particular "young boy or girl". No obligation whatsoever. We, as the audience, are NOT entitled to be satisfied on that score--ever. We merely have the right to agree or disagree with what we see and say so.