The difference is down to writing. Yes, the Witcher series hasn't been graced with absolutely stellar writing ("lesbomancy!" comes to mind, though it's still pretty funny since it's delivered by a dwarf in an otherwise bleak and horrible world) but it is still way above Kojima's level.
How do I know this? Aside from my avatar indicating bias, let's look at the way these games pace out their emotional peaks and troughs.
Witcher 2 has a quest where you run around gathering harpy feathers for an unspecified reason, culminating in this:
Whereas MGS can't stop with it's absurdity, what with how Snake recognises a soldier through their butt, the wolf with the eyepatch, Otacon's "japanese animes", Revolver Ocelot...etc. etc.
The humour feels much more unrefined and all over the place, making it more absurd. Witcher 2 on the other hand, has a few, select moments that truly drive the point home, like the vampire moment in the recent trailer.
So where am I going with this? Simply put, the quality of writing and context determines who gets a free pass. The Witcher has shown a level of maturity to match its setting and it has been shown to have high standards of writing. MGS hasn't shown either, and more often than not, resorts in syne-waving inconsistently between "lol random" and "war is hell".
So when CDProjektRed decides to talk about rape or it depicts heterosexuality, it's merited since we can trust them to deal with it maturely: they have come far from the Witcher 1, to the point where all the sex scenes in The Witcher 2 are optional and of those, there are tasteful ones that build character development and show Geralt & Triss' relationship in an adult but also human manner. Sex isn't "srs bzns" nor is it entirely "lol BEWBS", but a mix of both.
Kojima hasn't demonstrated that level of maturity. It also doesn't help that the first new female character in MGS V that we meet is a glamour model who never speaks and that Kojima made that cosplay comment. Judging by his past history of The Beauty and The Beast Unit...yeah, it doesn't bode well. People are getting rightfully tired of this, and the inconsistent writing would make it a stretch to say that there's something meaningful behind this presentation of women.
That'd be like saying that Hideaki Anno isn't just milking NGE fans by releasing the rebuilds.
So yeah, that's why CDProjektRed gets a free pass and Kojima doesn't.