There is nothing wrong with having a sexual, scantily clad character, particularly if they are used sensibly and coherently within the narrative of the story, which is what Kojima seems to be implying that he does....
However, I struggle to think of a female game model in the MGS series that wasn't ridiculously sexualized, often for no reason or atleast were very sexual. Why did Sniper Wolf feel she had to have an open cleavage in fucking Antarctica? Meryl's ass was a plot point, and her (supposed) asexuality was hammered on while constantly remarking things like how she doesn't wear a bra. In MGS2, Fortune wore a leather leotard and nothing else the entire game. Emma was mostly covered up, which is good because she looks like she's 13 otherwise, but all she went on was about how much she wanted to bone otacon. Olga is probably the only one, but she also spends most of the game disguised as a man, so sexualizing her would have been a giveaway (that said, who wants to bet that Snake discovered her secret by closely watching Mr. X's ass?). MGS3 we have Eva, who is obviously sexual and the Boss who remained unsexualized until the end where she undid her shirt for no real reason except extremely forced visual symbolism. And then MGS4 went all out with the perviness when Kojima went out of his way to oogle women who are suppose to be traumatized, mentally handicapped women (The B&B corp was the dumbest thing ever), while also putting special attention towards Naomi's undone shirt and Mei Ling's ass. The only female character in MGS4 that wasn't sexualized was Sunny (an 10 year old girl) and perhaps the FROGS (if they even count as characters). Most other women, like Para-Medic, are in the codec window, where it's harder to show them off. And even then, he managed to do it with Rosemary with the tit flipping feature on the PS3 controller. I didn't play Peace Walker or the other MGS games, but there is Paz and I'm sure that she's not the only one.
Sexualization isn't necessarily bad. In some cases, the sexualization can add to the character (In MGS4, Snake perving on Mei Ling's ass despite her being sensibly dressed is a character statement enforcing how decayed he is. Contrast how effortlessly he flirted with her in the opening of the first game and now he's reduced to immaturely peaking at her butt when she drops a pen. It's a shame that Mei Ling's sexualization is a statement on a male character rather than Mei Ling herself, but my point is that it can be used effectively in a narrative space.). And in Eva's case, given her backstory and goals, she can't be anything other than sexual to accomplish her mission. And, to his credit, Kojima also unnecessarily sexualizes men (Liquid not wearing a shirt ever (also in Antarctica), Vamp, the Snakes, and Raiden), not to the same extent, but that he puts in the effort for equal treatment is commendable, I suppose.
But he can't seriously get surprised that people think he's just sexualizing a women for no reason when that's what he's been doing for 15 years. Even if he has given Quiet plenty of narrative justification for it, like he did with Eva, it's ridiculously to take him at his word that this is a matter of artistic integrity rather than exploiting sexuality for an audience given his history or his own perving.